Use of novel biomarkers for detection of testicular carcinoma in situ and derived cancers in human samples

ABSTRACT

The present invention relates to methods and kits for identification of testicular carcinoma in situ (CIS), gonadoblastoma (a CIS-like pre-cancerous lesion found in dysgenetic gonads) and CIS-derived cancers based on at least one of the biomarkers included in the invention. It also relates to diagnosis of a subject&#39;s status of the testicular carcinoma in situ and the derived cancers based on the measurement of a relative abundance of one of the biomarkers.

FIELD OF THE INVENTION

The present invention provides biomarkers that characterize testicular carcinoma in situ (CIS), which is the precursor for classical testicular seminoma and non-seminomas. The same biomarkers may also be used to characterize gonadoblastoma, a CIS-like pre-cancerous lesion found in dysgenetic gonads.

BACKGROUND OF THE INVENTION

Testicular carcinoma in situ (CIS) is the common precursor of nearly all testicular germ cell tumors (TGCTs) that occur in young adults. The incidence of TGCTs has increased markedly over the past several decades, and these tumors are now the most common type of cancer in young men.

CIS cells may transform into either a seminoma or a non-seminoma. The seminoma retains a germ-cell-like phenotype, whereas the tumour known as non-seminoma or teratoma retains embryonic stem cell features; pluripotency and the ability to differentiate into virtually all somatic tissues. Non-seminomas comprise embryonal carcinoma (EC), various mixtures of differentiated teratomatous tissue components and extraembryonic tissues, such as yolk sac tumour and choriocarcinoma. In addition to CIS, gonadoblastoma, a CIS-like lesion occurs in dysgenetic testes and intersex gonads, which frequently may contain some ovarian structures.

The only difference between CIS and gonadoblastoma concerns the overall architecture of the lesion in the surrounding gonad (CIS is found usually in single rows along the basement membrane and there is a single layer of Sertoli cells between CIS cells and the lumen of seminiferous tubules, while gonadoblastoma contains nests (clumps) of CIS-like cells surrounded by small somatic granulosa-like cells and sometimes spermatogonia-like cells). The morphology and gene expression patterns of CIS cells and gonadoblastoma cells are indistinguishable (Jørgensen et al. Histopathology 1997), therefore, further in this application, the present inventors use the term CIS for both precursor lesions.

The most commonly used marker for CIS in clinical practice is placental-like alkaline phosphatase (ALPP or PLAP) (Manivel, J C, et al. Am J Surg Pathol 1987, 11:21-9), which is also a known marker of primordial germ cells. Epidemiological evidence and evidence

germ cells indicate that CIS is an inborn lesion, probably arising from gonocytes in early fetal life and progress to an overt TGCT after puberty. The precise nature of the molecular events underlying the initiation of malignant transformation from the gonocyte to the CIS cell has not yet been elucidated, and the following progression into overt tumors remains largely unknown.

In order to identify new markers for early detection of CIS, the present inventors analyzed gene expression in CIS cells and tumors in a systematic manner, by employing both a differential display (DD) methodology and by using a cDNA microarray covering the entire human transcriptome.

SUMMARY OF THE INVENTION

In the microarray studies the present inventors have circumvented detecting changes of gene expression not related to CIS (as CIS cells constitute only a small percentage of cells in a typical tissue sample) by using testis tissues containing different amounts of tubules with CIS and searched for genes regulated in a manner proportional to the content of CIS in the sample.

Selected candidates for CIS and tumor markers from both the DD and the microarray study have been verified by semi-quantitative reverse transcriptase PCR (RT-PCR) and the expressing cell type determined by in situ hybridization. Furthermore, the present inventors use antibodies against the some promising candidates and used immunohistochemistry to identify the expressing cell types in tissues with CIS/gonadoblastoma and in tumors derived from CIS.

The present inventors also investigated the gene expression profile (using the same large cDNA microarray) of testicular seminoma and embryonic carcinoma (EC, an undifferentiated component of non-seminomas) and compared that to the expression profile of CIS.

This facilitated identification of genes that mark the progression of CIS into either the seminoma or the non-seminoma. Results were confirmed by RT-PCR and markers were localized to tumor cells by in situ hybridization as well as for selected markers at the protein level by immunohistochemistry.

Carcincoma in situ (CIS) is the common precursor of histologically heterogeneous testicular germ cell tumors, which have markedly increased in frequency in the recent decades and

expression profiling, the present inventors identified more than 200 genes highly expressed in testicular CIS, including many never reported in testicular neoplasms. Expression was further verified by semi-quantitative RT-PCR and in situ hybridization, and by immunohistochemistry for a few protein products, for which antibodies were available.

DESCRIPTION OF THE INVENTION

The biomarkers disclosed herein can be used for the detection of CIS and gonadoblastoma but also biomarkers for the detection of the seminomas and non-seminomas derived from CIS and thus for the progression of CIS is included in the present invention.

The biomarkers were identified using differential display and genome-wide cDNA microarray analysis and subsequent verified by other methods, including in situ hybridization, which showed that the CIS markers were expressed in CIS cells.

For some biomarkers localization to CIS cells and some CIS-derived overt tumours was also done at the protein level by immunohistochemistry.

The present invention thus relates to the use of the identified biomarkers to identify CIS and the status of CIS derived cancers in human samples such as semen samples, blood, testicular biopsies, and biopsies from any other human tissue.

In one aspect, the present invention relates to a method for determining the presence of precursors of germ cell tumours in an individual. Such a diagnostic method would comprise determining the expression profile of a group of markers in a sample, and concluding from said expression profile whether or not the sample contains precursors of germ cell tumours, wherein the group of markers consists of markers selected independently from the markers listed in table 1, whereby the number of markers in the group is between one and the total number of markers listed in table 1.

Specifically, the method comprises the following steps:

-   -   a) determining the expression profile of a group of markers in         said sample, wherein the group of markers consists of at least         one marker selected independently from the markers listed in         table 1;     -   b) comparing said expression profile with a reference expression         profile;     -   c) identifying whether the expression profile is different from         said reference expression profile and         evaluating whether the sample contains precursors of germ cell         tumours if the expression profile is different from the         reference expression profile.

In the present context the term “precursors of germ cell tumours” relates to the commonly accepted fact that CIS is a common precursor for all germ cell tumours of the adolescents and young adults. CIS is also known as intratubular germ cell neoplasia of the unclassified type, testicular intraepithelial neoplasia and gonocytoma in situ, with the last term probably the most accurate from the biological point of view.

In the present context the term “expression profile” relates to assaying the level of transcripts, such as mRNA, either relative to a reference value, relatively to another transcript or sample and/or absolutely values. In example cDNA micro arrays measure the abundance of a transcript in two different samples relative to each other, whereas e.g. real-time PCR measures the absolute copy number of transcripts in the sample. Both relative and absolute measurements enables a person skilled in the art to make a diagnostic decision based on the data presented.

As known to the skilled addressee, an expression profile of a transcript could also be obtained from e.g. amplified RNA, aRNA, and/or complementary DNA, cDNA, by various techniques. Thus, the present invention also relates to any methods using such manipulations. The genes listed in table 1 are in no particular order, and thus both the listed and the complementary strand is an object of the present inventions.

The sequences listed in table 1, may represent only a part of the sequence of the gene listed, e.g. an EST sequence, fragment of sequence or similar. However, the full genomic sequence, the coding sequence, untranslated regions, and promoter regions is an object of the present invention.

In general, assaying the level of transcripts, and thus determining the expression profile of a group of markers can be made by several technical approaches, such as, but not limited to, micro arrays, filter arrays, DNA chips, gene chips, differential display, SAGE, northern blot, RT-PCR, quantitative PCR, PCR, real-time PCR or any other known technique known to the skilled addressee

When assaying levels of expression of the sequences presented in table 1, the levels refers

nucleic acid is determined by methods well known in the art. “Differentially expressed” or “changes in the level of expression” may refer to an increase or decrease in the measurable expression level of a given nucleic acid and “Differentially expressed” when referring to microarray analysis means the ratio of the expression level of a given nucleic acid in one sample and the expression level of the given nucleic acid in another sample is not equal to 1.0. “Differentially expressed” when referring to microarray analysis according to the invention also means the ratio of the expression level of a given nucleic acid in one sample and the expression level of the given nucleic acid in another sample is greater than or less than 1.0 and includes greater than 1.2 and less than 0.7, as well as greater than 1.5 and less than 0.5. A nucleic acid also is said to be differentially expressed in two samples if one of the two samples contains no detectable expression of the nucleic acid.

Absolute quantification of the level of expression of a nucleic acid can be accomplished by including known concentration(s) of one or more control nucleic acid species, generating a standard curve based on the amount of the control nucleic acid and extrapolating the expression level of the “unknown” nucleic acid species from the hybridization intensities of the unknown with respect to the standard curve. The level of expression is measured by hybridization analysis using labeled target nucleic acids according to methods well known in the art. The label on the target nucleic acid can be a luminescent label, an enzymatic label, a radioactive label, a chemical label or a physical label. Preferably, target nucleic acids are labeled with a fluorescent molecule. Preferred fluorescent labels include, but are not limited to, fluorescein, amino coumarin acetic acid, tetramethylrhodamine isothiocyanate (TRITC), Texas Red, Cy3 and Cy5.

Concluding from said expression profile whether or not the sample contains precursors of germ cell tumours can be obtained by assaying the expression profile and determine if the markers are either present and/or up-regulated and/or down-regulated. Depending on the experimental set-up the marker genes may appear up-regulated but could also appear down-regulated, if e.g. the ratio were switched. The settings in the present application focus on the up-regulated markers.

Depending on the assay method and set-up the measurement of the marker genes may be done in reference to either another transcript, a sample or measured absolutely.

The group of markers consists of markers selected independently from the markers listed in table 1, the number of markers in the group is between one and the total number of markers listed in table 1, such as 1 marker, 2 markers, 3 markers, such as 4 markers, such as 5 markers, e.g. 6 markers, 7 markers, 8 markers, such as 9 markers, e.g. 10

markers, such as 16 markers, such as 17 markers, e.g. 18 markers, 19 markers, e.g. 20 markers, such as 21 markers, 22 markers, 23 markers, e.g. 24 markers, such as 25 markers, such as 30 markers, such as 40 markers, e.g. 50 markers, such as 60 markers, such as 70 markers, e.g. 80 markers, e.g. 90 markers, such as 100 markers, such as 120 markers, e.g. 140 markers, such as 150 markers, e.g. 170 markers, e.g. 200 markers, e.g. 220 markers, e.g. 240 markers, such as 255 markers.

The term “sample” could be a semen sample, a blood sample, a serum sample, a urine sample, a testicular biopsy sample, or a biopsy from any other human tissue. The marker genes described here may be used to identify CIS or seminoma or non-seminoma cells in other clinical samples than those related to the testis and semen samples, i.e. in extra-gonadal brain tumors or blood samples from patients with disseminated seminoma.

In a presently preferred embodiment the sample is a semen sample.

The general scope of the present invention relates to detection of precursors of germ cell tumours in various samples as described above. It is obvious to the skilled addressee that the methods described herein enables a person skilled in the art to detect the presence of and/or the development of even very small amounts of precursors of germ cell tumours in the selected samples. In a presently preferred embodiment the methods described herein enables detection of at least one cell which is a precursors of germ cell tumours.

The expression profiles and as described below the intensity values are indicative of precursors of germ cell tumours since these data are found significantly more often in patients with a precursors of germ cell tumours than in patients without the precursors of germ cell tumours.

As used herein, “expression pattern” or “expression profile” comprises the pattern (i.e., qualitatively and/or quantitatively) of expression of one or more expressed nucleic acid sequences where one or more members of the set are differentially expressed.

As the skilled addressee would recognise the present invention enables a person skilled in the art in both diagnosing and/or monitoring precursors of germ cell tumours in a patient by detecting the expression level(s) of one or more genes described in table 1.

The present invention also relates to use of any of the sequences/genes/mRNAs listed in the present application for diagnostics of precursors of germ cell tumours located in the testis or in all other locations, using any method that can detect the products on the mRNA

Western blot, protein-microarrays etc.) in any human samples including semen samples, blood, tissue samples, urine, etc. in patients or healthy individuals, the sequences selected from the group consisting of SEQ ID NO 1-255 are of particularly value.

In other words, the present invention relates to a method for diagnosing precursors of germ cell tumours, the method comprising the steps of assaying an expression level for each of a predetermined number of markers of precursors of germ cell tumours in a sample; and, identifying said precursors of germ cell tumours if at least one of said expression levels is greater than a reference expression level.

Alternatively, the method for determining the presence of precursors of germ cell tumours in a sample may be based on measurements of the polypetides expressed by the nucleotide sequences comprising the markers selected from the group of SEQ ID NO: 1 to SEQ ID NO:255.

Thus, another aspect of the present invention relates to a method for determining the presence of precursors of germ cell tumours in an individual comprising determining the intensity signal(s) of a group of markers in a patient sample, and concluding from said intensity signal(s) whether the patient sample contains of precursors of germ cell tumours, wherein the group of markers consists of markers selected independently from the markers listed in table 1, whereby the number of markers in the group is between one and the total number of markers listed in table 1.

Such a method comprises the following steps:

-   -   a) determining the intensity signal of the proteins encoded by         each of the members of the group of markers in said sample,         wherein the group of markers consists of at least one marker         selected independently from the markers listed in table 1     -   b) comparing each individual intensity signal with a         corresponding reference intensity signal;     -   c) identifying whether each individual intensity signal is         different from said corresponding reference intensity signal and         evaluating whether the sample contains precursors of germ cell         tumours if the intensity signal is different from the         corresponding reference intensity signal.

The term “intensity signal” relates to assaying the protein level of the proteins encoded by the transcripts from table 1. Any immuno-assay is able to perform such measurement e.g. ELISA, RIA, Western blots, or dot blots. Also other methods capable of measuring the amount of a protein quantitatively or relatively. Such techniques include, but are not limited to; mass spectrometry base measurements, protein microarrays, ProteinChip® (Ciphergen) and derived methods.

As exemplified below, the present inventors are generating antibodies against the gene products of the present inventions. FIG. 6 displays an example of one such antibody used in an immuno-staining of an tissue section comprising CIS cells.

Antibodies generated against the gene products of the present invention may enable monitoring of metastasis and invasion of germ cell tumours.

As shown in table 1, several markers are up-regulated in highly abundant CIS cells, thus in one embodiment, the present invention can be performed on such up-regulated markers. Such specific markers are the markers selected from the group consisting of SEQ ID NO 1-157.

A presently preferred embodiment of the present invention further relates to a method according to the invention, wherein the group of markers consists of at least one marker which in a sample with CIS in 100% of the seminiferous tubules is up-regulated more than 7 fold when compared to a reference sample, such as 7.1 fold, e.g. 7.2 fold, such as 7.5 fold, e.g. 8 fold, e.g. 9 fold, such as 10 fold, e.g. 11 fold, e.g. 12 fold, such as 13 fold, 14 fold, 15 fold, e.g. 16 fold, such as 17 fold, 18 fold, 19 fold, e.g. 20 fold, such as 25 fold, e.g. 30 fold, 35 fold, 40 fold, e.g. 45 fold, such as 50 fold, e.g. 55 fold, e.g. 60 fold, such as 65 fold, e.g. 70 fold, such as 75 fold, e.g. 80 fold, such as 85 fold, e.g. 90 fold, e.g. 95 fold, such as 100 fold.

In another embodiment of the present invention some markers are, in an sample with CIS in 100% of the seminiferous tubules, up-regulated more than 4.3 fold but less than 7 fold. Such markers are presently considered as medium-potential markers, thus the applicability of these markers are considered to be less useful than the markers with higher abundance in CIS cells.

In yet another embodiment of the present invention some markers are, in a sample with CIS in 100% of the semiferous tubules, up-regulated more than 3 fold but less than 4.3 fold. Such markers are presently considered as markers of lesser potential, thus the

markers with higher abundance in CIS cells, however still capable of adding valuable information for the purposes of the present invention.

Another presently preferred embodiment of the present invention relates to a method according to the invention, wherein the expression profile distinguishes between classical testicular seminoma and testicular non-seminoma in gonads or in extra-gonadal localizations.

When the present inventors compared tissue samples comprising non-seminoma (EC-cells) versus CIS cells and seminoma cells, the markers defined in SEQ ID NO 158 to SEQ ID NO 202 showed an up-regulation of more than 5 fold, whereas the CIS cells and seminoma cells showed an up-regulation of less than 2 fold.

Thus, the markers defined in SEQ ID NO 158 to SEQ ID NO 202 enable a person skilled in the art to distinguish non-seminoma from CIS and seminoma, since these markers are all upregulated in non-seminoma as described in table 1 and the examples below, when compared to samples containing CIS and/or seminoma.

When the present inventors compared tissue comprising seminoma cells versus CIS cells and non-seminoma cells, the markers defined in SEQ ID NO 203 to SEQ ID NO 255 showed an up-regulation of more than 3 fold, whereas the CIS cells and non-seminoma cells showed an up-regulation of less than 2 fold.

Thus, the markers defined in SEQ ID NO 203 to SEQ ID NO 255 enable a person skilled in the art to distinguish classical seminoma from CIS and/or non-seminoma, since these markers are all upregulated in seminoma as described in table 1 and the examples below, when compared to samples containing CIS and/or non-seminoma.

One presently preferred embodiment relates to a method which can distinguish seminoma from non-seminoma.

Another presently preferred embodiment relates to a method which can distinguish seminoma from CIS.

Yet another presently preferred embodiment relates to a method which can distinguish non-seminoma from CIS.

Therefore, one aspect of the present invention relates to a method for monitoring

comprising determining the expression profile and/or the intensity signal(s) of a group of markers in a sample and concluding from expression profile and/or the intensity signal(s), whether the sample contains precursors of germ cell tumours, wherein the group of markers consists of markers selected independently from the markers listed in table 1, whereby the number of markers in the group is between one and the total number of markers listed in table 1.

In one detailed embodiment the method comprises the following steps:

-   -   a) determining the expression profile of a group of markers in         said sample, wherein the group of markers consists of at least         one marker selected independently from the markers listed in         table 1;     -   b) comparing said expression profile with a reference expression         profile;     -   c) identifying whether the expression profile is different from         said reference expression profile and         evaluating the development stage of precursors of germ cell         tumours to overt cancer cells if the expression profile is         different from the reference expression profile.

Alternatively, the method comprises the following steps:

-   -   a) determining the intensity signal of the proteins encoded by         each of the members of the group of markers in said sample,         wherein the group of markers consists of at least one marker         selected independently from the markers listed in table 1     -   b) comparing each individual intensity signal with a         corresponding reference intensity signal;     -   c) identifying whether each individual intensity signal is         different from said corresponding reference intensity signal and         evaluating the development stage of precursors of germ cell         tumours to overt cancer cells if the intensity signal is         different from the corresponding reference intensity signal.

In yet another aspect, the present invention relates to a method for identifying precursors of germ cell tumours in a sample from a mammal, the method comprising

-   -   assaying said sample by a quantitative detection assay and         determining the expression profile and/or the intensity         signal(s) of at least one marker selected from the group         consisting of

SEQ ID NO: 1 to SEQ ID NO: 255

-   -   comparing said expression profile and/or the intensity signal(s)         with reference value(s)     -   identifying whether the expression profile and/or the intensity         signal(s) of at least one marker from the sample is         significantly different from the reference value, and         evaluating whether the sample contains precursors of germ cell         tumours if the expression profile and/or the intensity signal(s)         is different from the reference value.

As the skilled addressee would recognise the present invention is useful as a method for determining the presence of precursors of germ cell tumours in an individual comprising detecting the presence or absence of at least one expression product, wherein said at least one expression product comprise a nucleotide sequence selected from the group consisting of SEQ ID 1-255 in a sample isolated from the individual.

In another aspect, the present invention also relates to a method of assessing the efficacy of a therapy for inhibiting precursors of germ cell tumours in a subject, the method comprising

-   -   comparing the expression profile of a group of markers in a         first sample obtained from the subject prior to providing at         least a portion of the therapy to the subject and the expression         profile of a group of markers in a second sample obtained from         the subject following provision of the portion of the therapy,         wherein a significantly altered expression profile of the         marker(s) in the second sample, relative to the first sample, is         an indication that the therapy is efficacious for inhibiting         precursors of germ cell tumours in the subject         wherein the group of markers consists of markers selected         independently from the markers listed In table 1 and whereby the         number of markers in the group is between one and the total         number of markers listed in table 1.

Alternatively, the above method aspect can also be assessed by comparing the intensity signals of the proteins encoded by each of the member of the group of markers instead of comparing the expression profiles.

The method of assessing the efficacy of a therapy of the present invention also relates to methods for identifying, evaluating, and monitoring drug candidates for the treatment of precursors of germ cell tumours and of course any of the later stages. According to the invention, a candidate drug or therapy is assayed for its ability to decrease the expression of one or more markers of precursors of germ cell tumours. In one embodiment, a specific drug or therapy may reduce the expression of markers for a specific type or subclass of precursors of germ cell tumours described herein. Alternatively, a preferred drug may have a general effect on precursors of germ cell tumours and decrease the expression of different markers characteristic of different types or classes of precursors of germ cell tumours. In one embodiment, a preferred drug decreases the expression of a precursors of germ cell tumours marker by killing precursors of germ cell tumour cells or by interfering with their replication.

Current trends in stem cell research enable a person skilled in the art of various treatments comprising transplanting or regeneration of tissue by the use of e.g. embryonal stem cells.

In the present application the present inventors have identified that CIS cells have many features, which are embryonal stem cell like, see FIG. 4 and FIG. 5 and the examples below.

CIS cells thus both are embryonal stem cell like and cancer precursor cells. Thus, by use of the present markers a person skilled in the art would be able to judge, if the e.g. tissue derived from embryonal stem cells contains cells, which are likely to become cancer precursor cells, and thus represent valuable information for consideration before transplanting e.g. an embryonal stem cells.

In another aspect, the present invention also relates to a methods for analysing the presence of undifferentiated stem cells highly likely to progress to precursors of germ cell tumours and/or cancer in an individual.

Such methods comprise the following steps in one embodiment:

-   -   a) determining the expression profile of a group of markers in         said sample, wherein the group of markers consists of at least         one marker selected independently from the markers listed in         table 1;     -   b) comparing said expression profile with a reference expression         profile;     -   c) identifying whether the expression profile is different from         said reference expression profile and         evaluating whether the sample contains undifferentiated stem         cells highly likely to progress to precursors of germ cell         tumours and/or cancer in the individual if the expression         profile is different from the reference expression profile.

Alternatively, such methods comprise the following steps in a second embodiment:

-   -   a) determining the intensity signal of the proteins encoded by         each of the members of the group of markers in said sample,         wherein the group of markers consists of at least one marker         selected independently from the markers listed in table 1     -   b) comparing each individual intensity signal with a         corresponding reference intensity signal;     -   c) identifying whether each individual intensity signal is         different from said corresponding reference intensity signal and         evaluating whether the sample contains undifferentiated stem         cells highly likely to progress to precursors of germ cell         tumours and/or cancer in the individual if the intensity signal         is different from the reference expression profile.

Testicular carcinoma in situ (CIS) is the common precursor of nearly all testicular germ cell tumors (TGCTS) that occur in young adults. The incidence of TGCTs has increased markedly over the past several decades, and these tumors are now the most common type of cancer in young men, thus representing an increasing health problem. There is a current need in the art of potential screening methods to identify the patients in an early non-invasive stage for the purpose of e.g. treatment strategy.

Thus, in another aspect, the present invention also relates to a method for screening for the presence of precursors of germ cell tumours in an individual of a population, said method comprising determining the expression profile and/or the intensity signal(s) of a group of markers in a sample obtained from said individual, and concluding from the expression profile and/or the intensity signal(s) whether the sample contains at least one precursor cell of germ cell tumours, wherein the group of markers consists of markers selected independently from the markers listed in table 1, whereby the number of markers in the group is between one and the total number of markers listed in table 1.

Tested Individual Markers

A range of the genes listed in table 1 has been further investigated at the protein level. Initially the genes from FIG. 1 which are highly expressed at the RNA level were studied at the protein level on tissue sections containing CIS using immunohistochemical detection. The antibodies which stained only CIS or tumour-cells in testicular tissue sections were further used to stain semen samples spreads (cytospins) on a microscope slide.

One embodiment of the present invention relates to a method according to the present invention, wherein the marker is selected from the group consisting of AP-2γ, NANOG, TCL1A, PIM-2, and E-cadherin.

AP-2γ

AP-2γ is encoded by the TFAP2C gene mapped on chromosome 20q13.2 and is a member of a family of DNA-binding transcription factors, which includes AP-2α, AP-2β, AP-2γ, TFAP-2δ and TFAP-2ε. During vertebrate embryogenesis, these proteins play important roles in the development and differentiation of the neural tube, neural crest derivatives, skin, heart and urogenital tissues and show overlapping, but distinct, patterns of expression within these tissues.

AP-2γ is required within the extra-embryonic lineages for early post-implantation development, but apparently does not play an autonomous role within the embryo proper. Mice lacking AP-2γ die at day 7.5-8.5 post coitum due to malformation of extra-embryonic tissues.

In the above genome-wide gene expression profiling study of CIS cells, we have identified a number of genes expressed also in embryonic stem cells and foetal gonocotes but not in adult germ cells, thus providing many possible new markers for CIS. One of such genes was TFAP2C (mapped to chromosome 20q13.2), which encodes the transcription factor activator protein-2 (AP-2γ).

By immunhistochemical detection of the AP-2γ protein the present inventors investigated the protein expression in a large range of tissues including fetal and malignant tissues. The present inventors found that AP-2γ protein expression was very restricted and only found in early gonocytes and other not fully differentiated cells. Also it was found to be very solid nuclear marker of testicular CIS cells and derived neoplastic cells (FIG. 6).

The present inventors disclose AP-2γ as a novel marker for foetal gonocytes and neoplastic germ cells, including testicular CIS, with a role in pathways regulating cell differentiation and a possible involvement in oncogenesis.

The fact that AP-2γ protein was not expressed in normal adult reproductive tract but was abundant in nuclei of CIS and tumour cells, which are better protected than the cytoplasm from degradation in semen due to a structural strength, prompted us to analyse the value of AP-2γ for detection of CIS and/or tumour cells in ejaculates in a series of patients and controls.

In an investigation of 104 andrological patients, presented in Example 10, cells positive for AP-2γ were found only in semen samples from patients diagnosed a priori with testicular neoplasms and, surprisingly, in a 23-year-old control subject with oligozoospermia and no symptoms of a germ cell tumour (FIG. 7).

Testicular biopsies performed during the follow-up of the 23-year-old control subject revealed widespread CIS in one testis, thus proving a diagnostic value of the new assay. Optimisation of the method is in progress, but a preliminary assessment suggests that the method may have a place in screening of germ cell neoplasia in at-risk patients. The local ethics committee approved the studies of AP-2γ expression and participants gave written informed consent.

The number of patients that we have screened for the presence of immunoreactive AP-2γ is continuously increasing as we are testing patients as they appear in our clinic. So far we have tested 347 andrological patients (including the 104 mentioned above) and found CIS-like cells positive for AP-2γ in semen samples of 3 patients, including the first case described above (a 23-year-old subfertile control subject with widespread CIS confirmed by testicular biopsies). Two other patients are currently under clinical follow-up and being considered for testicular biopses.

Thus, in a particular preferred embodiment, the present invention relates to a method according to the present invention, wherein the marker is AP-2γ.

TCL-1A

TCL1A is a powerful oncogene that, when overexpressed in both B and T cells, predominantly yields mature B-cell lymphomas. TCL1A both in vitro and in vivo, increase AKT kinase activity and as a consequence enhances substrate phosphorylation. In vivo, TCL1A stabilizes the mitochondrial transmembrane potential and enhances cell proliferation and survival. TCL1 forms trimers, which associate with AKT in vivo and TCL1A is thus an AKT kinase coactivator that promotes AKT-induced cell survival and proliferation.

Expression of the TCL1A protein in testicular CIS as detected by immunohistochemical staining is shown in FIG. 8.

In another particular preferred embodiment, the present invention relates to a method according to the present invention, wherein the marker is TCL-1A.

NANOG

Nanog-deficient Mouse inner cell mass (ICM) fail to generate epiblast and only produce parietal endoderm-like cells. Mouse Nanog-deficient embryonic stem (ES) cells loose pluripotency and differentiate into extraembryonic endoderm lineage. Nanog is thus a critical factor in maintaining pluripotency in both ICM and ES cells.

Elevated Nanog expression from transgene constructs is sufficient for clonal expansion of ES cells, bypassing Stat3 and maintaining POU5F1 (Oct4) levels.

NANOG was found to be highly expressed in CIS both at the RNA and protein level. Immunohistochemical detection of NANOG is shown in FIG. 9 and at the RNA level in FIGS. 1, 2, and 3.

In another particular preferred embodiment, the present invention relates to a method according to the present invention, wherein the marker is NANOG.

PIM-2 and E-cadherin

Similar to AP-2γ, TCL1A, and NANOG, the proteins encoded by the E-cadherin gene and the PIM-2 oncogene were also found highly expressed in CIS cells. Immunohistochemical detection of E-cadherin is shown in FIG. 10 and PIM-2 in FIG. 11.

In another particular preferred embodiment, the present invention relates to a method according to the present invention, wherein the marker is PIM-2 and/or E-cadherin.

Antibodies directed against the proteins encoded by the genes in table 1 were used for immunohistochemical investigations on sections from different tissues including testicular CIS.

The present application furthermore particularly relates to a method according to the present invention, wherein the intensity signal is determined by immunocytological detection (immuno staining).

As the skilled person will know, any of the methods of the present invention may be used for screening for the presence of precursors of germ cell tumours in individual of a population, either alone or in any combination.

In another aspect, the present invention also relates to a kit for use in an assay or method as defined in the present application.

In one embodiment, such kit may be a diagnostic array comprising: a solid support; and a plurality of diagnostic agents coupled to said solid support, wherein each of said agents is used to assay the expression level of at least one of the markers shown in table 1, wherein each of said diagnostic agents is selected from the group consisting of PNA, DNA, and RNA molecules that specifically hybridize to a transcript from a marker of precursor of germ cell tumours or wherein each of said diagnostic agents is an antibody that specifically binds to a protein expression product of a marker of precursor of germ cell tumours.

In another embodiment, the present invention further provides databases of marker genes and information about the marker genes, including the expression levels that are characteristic of precursor of germ cell tumours. According to the invention, marker gene information is preferably stored in a memory in a computer system. Alternatively, the information is stored in a removable data medium such as a magnetic disk, a CDROM, a tape, or an optical disk. In a further embodiment, the input/output of the computer system can be attached to a network and the information about the marker genes can be transmitted across the network.

Preferred information includes the identity of a predetermined number of marker genes the expression of which correlates with a particular type of precursor of germ cell tumours. In addition, threshold expression levels of one or more marker genes may be stored in a

expression level is a level of expression of the marker gene that is indicative of the presence of a particular type or class precursor of germ cell tumours.

In a preferred embodiment, a computer system or removable data medium includes the identity and expression information about a plurality of marker genes for several types or classes of precursor of germ cell tumours disclosed herein. In addition, information about marker genes for normal testis tissue may be included. Information stored on a computer system or data medium as described above is useful as a reference for comparison with expression data generated in an assay of testis tissue of unknown disease status

It should be understood that any feature and/or aspect discussed above in connection with the methods according to the invention apply by analogy to the uses according to the invention.

All patent and non-patent references cited in the present application, are hereby incorporated by reference In their entirety.

As will be apparent, preferred features and characteristics of one aspect of the invention may be applicable to other aspects of the invention.

Throughout this specification the word “comprise”, or variations such as “comprises” or “comprising”, will be understood to imply the inclusion of a stated element, integer or step, or group of elements, integers or steps, but not the exclusion of any other element, integer or step, or group of elements, integers or steps.

The invention will hereinafter be described by way of the following non-limiting Figures and Examples.

FIGURE LEGENDS

FIG. 1

Hierarchical clustering of genes found by filtering data so only genes 4 fold or more up-regulated in the sample with CIS in 100% of the tubules and 2 fold in the samples with 50 and 75% tubules with CIS. Hierarchical clustering was done using Euclidean distances and average linkage. Some redundancy between entries is seen and implies consistency in the results. The image clone number (Unique ID on the array) is reported in front of the gene names and can be used to search the German Resource Center for Genome Research for

FIG. 2

Further analysis of selected genes that in microarray study were found up-regulated in CIS. A) Examples of the semi-quantitative RT-PCR on a spectrum of testicular tissue samples. The gene name is on the right side of the panes. In the gels of NANOG, and POU5F1 the beta-actin-marker band of 800 bp is visible. Representative DNA fragments from all RT-PCR amplifications were excised, cloned, and sequence verified. 129142 is an Image clone number. B) Corresponding quantifications of NANOG and POU5F1 and the ratio between the two. Quantification was done by digitalizing the image of the agarose gel. M=100 base pair marker, SEM=seminoma, TER=teratoma, EC=embryonal carcinoma, CIS=testicular tissue showing 100% tubules with carcinoma in situ, NOR=normal testicular tissue, CIS A=CIS amplified for microarray analysis, H2O=control. The CIS sample (to the right) is the same sample used in the microarray analysis.

FIG. 3

Analysis of the cellular expression in tubules with CIS by in situ hybridization of NANOG, SLC7A3, TFAP2C and ALPL showing that the expression was confined to CIS cells (arrows). CIS cells are seen as a stained ring with a stained nucleus in the center, while the rest appears empty, due to large amounts of glycogen washed out during the tissue processing. Staining was in addition seen in Sertoli cells nuclei, probably due to over-staining necessary to visualize low abundance transcripts (arrows), since this was also seen with the sense probe. The sense control is from neighbouring sections of the same tubule as the anti-sense and inserted in the lower right corner. The scale bar corresponds to 50 μm.

FIG. 4

Genes from FIG. 1 reported to be up regulated in ESC. Data on mouse ESC are from Ramalho-Santos et al. (Ramalho-Santos, M, et al. Science 2002, 298:597-600) whereas data on human ESC are from Sato et al. (Sato, N, et al. Dev Biol 2003, 260:404-13) and Sperger et al. (Sperger, J M, et al. Proc Natl Acad Sci USA 2003, 100:13350-5). The overlap between genes reported in these studies and genes identified in CIS (FIG. 1) amount to roughly 35% but may be even greater due to differences in gene annotation and RNA references used.

FIG. 5

Chromosomal distribution of genes more than 2 fold up-regulated in the sample with 100% tubules having CIS. A) Distribution per chromosome and normalized by the size of the chromosomes (blue bars) or by the number of UniGene clusters on each chromosome (red bars). Chromosomal size was acquired from Ensembl, http://www.ensembl.org/, and number of UniGene clusters (Build 34 version 3) from NCBI, http://www.ncbi.nlm.nih.gov/. B) Detailed distribution of the number of up-regulated genes in each chromosomal band. The color-coding is outline in the inserted box.

FIG. 6.

Immuno-staining of transcription factor AP-2γ (TFAP2C) on a cross-section of testicular tissue containing both normal seminiferous tubules without CIS and tubules with CIS lesion. The CIS cells stain darkly and the signal is located to the nucleus of the CIS cells.

FIG. 7

A. Semen sample from a control patient spiked with CIS cells that are strongly stained with AP-2γ.

B1. AP-2γ-positive CIS cells in the semen sample of the 23-years-old subfertile control subject diagnosed with CIS by this assay.

B2, B3. Examples of AP-2γ stained cells in the 23-years-old subfertile control subject diagnosed with CIS by this assay, higher magnification.

C1, C2. Examples of AP-2γ stained cells in a patient known a priori to harbour testicular cancer.

D. Histological features of the biopsy of the left testis of the 23-years-old subfertile control subject with AP-2γ staining.

E. placental alkaline phosphatase (PLAP) staining showing CIS cells both adjacent to the tubular membrane and in the lumen. F. Semen sample from a control patient, with no AP-2γ-positive cells.

FIG. 8

Immuno-staining of TCL1A on a cross-section of testicular tissue containing tubules with CIS lesion. The CIS cells stain highly red and the signal is located to the nucleus of the CIS cells.

FIG. 9

Immuno-staining of homeobox protein NANOG on a cross-section of testicular tissue containing both normal seminiferous tubules without CIS and tubules with CIS lesion. The CIS cells stain darkly and the signal is located to the nucleus of the CIS cells.

FIG. 10

Immuno-staining of E-cadherin on a cross-section of testicular tissue containing tubules with CIS lesion. The CIS cells stain dark red and the signal is located to the cytoplasm or cellular membrane of the CIS cells.

FIG. 11

Immuno-staining of PIM-2 on a cross-section of testicular tissue containing tubules with CIS lesion. The CIS cells stain dark red and the signal is located to the nucleus of the CIS cells.

TABLE I IMAGE

 Entry [RZPD] clone Feature description

 ID No: IMAGp998N195554; IMAGp971M1993 2244690 Nanog homeobox

 ID No: IMAGp998G08223; IMAGp971H0410 147103 hXBP-1 transcription factor

 ID No: IMAGp998F08222; IMAGp971F0410 146695

 ID No: IMAGp998A06220; IMAGp971B0610 145805 TMF1 TATA element modulatory factor 1

 ID No: IMAGp998D203167; IMAGp971C1959 1258339 LIN28 lin-28 homolog (C. elegans)

 ID No: IMAGp998D054091; IMAGp971C0466 1613140 developmental pluripotency associated 5; embryonal

stem cell specific gene 1

 ID No: IMAGp998K241161; IMAGp971D2341 488207 Homo sapiens lung type-I cell membrane-

associated protein hT1a-2 (hT1a-2) mRNA

 ID No: IMAGp998J095673; IMAGp971I09130 2290280

 ID No: IMAGp998I175722; IMAGp971I1796 2309080

 ID No: IMAGp998J105673; IMAGp971E17130 2290281

 ID No: IMAGp998N115245; IMAGp971I0390 2126026 SLC7A3 solute carrier family 7 (cationic

amino acid transporter, y+ system), member 3

 ID No: IMAGp998J05529; IMAGp971I0522 245476

 ID No: IMAGp998A03577; IMAGp971A0324 263690

 ID No: IMAGp998H234408; IMAGp971G2474 1734982 FLJ10884 hypothetical protein FLJ10884

 ID No: IMAGp998G13226; IMAGp971F0610 148260

 ID No: IMAGp998J23134; IMAGp971H236 129142

 ID No: IMAGp998K225545; IMAGp971L2192 2241165

 ID No: IMAGp998N121162; IMAGp971O1341 488651 MGC16491 hypothetical protein MGC16491

 ID No: IMAGp998H07676; IMAGp971G1031 301878 SCGB3A2 secretoglobin, family 3A,

member 2

 ID No: IMAGp998B171780; IMAGp971G1744 725680 TFAP2C transcription factor AP-2 gamma

(activating enhancer binding protein 2 gamma)

 ID No: IMAGp998A2488; IMAGp971B232 111647 EFEMP1 EGF-containing fibulin-like

extracellular matrix protein 1

 ID No: IMAGp998H01154; IMAGp971C01113 32759 NFE2L3 nuclear factor (erythroid-derived

2)-like 3

 ID No: IMAGp998J02274; IMAGp971K01117 46959 Human pim-2 protooncogene homolog

pim-2h mRNA, complete cds

 ID No: IMAGp998L10121; IMAGp971M185 124569 Human normal keratinocyte substraction library

mRNA, clone H22a, complete sequence

 ID No: IMAGp998J075711; IMAGp971J1294 2304870 MYBL2 v-myb myeloblastosis viral

oncogene homolog (avian)-like 2

 ID No: IMAGp998N06536; IMAGp971P1522 248261 glycine dehydrogenase (glycine cleavage

system protein P)

 ID No: IMAGp998M17826; IMAGp971N1034 359608 LBP protein likely ortholog of mouse CRTR-1

 ID No: IMAGp998P11794; IMAGp971O0935 347386 RAB15 RAB15, member RAS onocogene

family

 ID No: IMAGp998O08148; IMAGp971M05112 30149 Human mRNA for liver-type alkaline

phosphatase

 ID No: IMAGp998C095623; IMAGp971I0993 2270912

 ID No: IMAGp998O205798; IMAGp971P1197 2337259 PRDM1 PR domain containing 1, with ZNF

domain

 ID No: IMAGp998A10192; IMAGp971B108 135057 UP uridine phosphorylase

 ID No: IMAGp998F20979; IMAGp971E2038 418195 ESTs, Weakly similar to hypothetical protein FLJ20378 [Homo

sapiens]

 ID No: IMAGp998B095717; IMAGp971C1895 2306984

 ID No: IMAGp998M125582; IMAGp971H07127 2255411 transcription factor CP2-like 1

 ID No: IMAGp998M154512; IMAGp971N1778 1844534

 ID No: IMAGp998M144547; IMAGp971G0981 1857973

 ID No: IMAGp998L105312; IMAGp971P0590 2151705 HLXB9 homeo box HB9

 ID No: IMAGp998D201008; IMAGp971D2339 429283 pleckstrin homology-like domain, family A,

member 3

 ID No: IMAGp998H065732; IMAGp971C0596 2312885

 ID No: IMAGp998H084295; IMAGp971G0772 1691575 COL22A1 collagen, type XXII, alpha 1

 ID No: IMAGp998F176102; IMAGp971E15132 2453776 NACHT, leucine rich repeat and PYD

containing 9

 ID No: IMAGp998K013431; IMAGp971J01106 1359864

 ID No: IMAGp998M23174; IMAGp971P24114 41558

 ID No: IMAGp998C17793; IMAGp971B1734 346696 Human transcription factor RTEF-1 (RTEF1)

mRNA, complete cds

 ID No: IMAGp998O144918; IMAGp971P13122 2000485 T-cell leukemia/lymphoma 1B or TCL6 T-

cell leukemia/lymphoma 6

 ID No: IMAGp998O021010; IMAGp971O0139 430297 Human E1A enhancer binding protein

(E1A-F) mRNA, partial cds

 ID No: IMAGp998E201114; IMAGp971J1941 470011 Human mRNA for fibroblast tropomyosin

TM30 (pl)

 ID No: IMAGp998H224299; IMAGp971D2472 1693125

 ID No: IMAGp998G195647; IMAGp971J18129 2280234

 ID No: IMAGp998K06166; IMAGp971K05114 38228 low density lipoprotein receptor-related

protein 4

 ID No: IMAGp998D03384; IMAGp971E0415 200018 H. sapiens mRNA for Tcell

leukemia/lymphoma 1

 ID No: IMAGp998E01223; IMAGp971D0610 147048 Homo sapiens endothelial cell protein

C/APC receptor (EPCR) mRNA, complete cds

 ID No: IMAGp998D054941; IMAGp971D0184 2009044

 ID No: IMAGp998A17115; IMAGp971B104 122008 long-chain fatty-acyl elongase

 ID No: IMAGp998K035709; IMAGp971J0394 2304122

 ID No: IMAGp998F13278; IMAGp971K05119 48538 ETV5 ets variant gene 5 (ets-related

molecule)

 ID No: IMAGp998B06202; IMAGp971A069 138917 Human L-myc protein gene, complete cds

 ID No: IMAGp998E1783; IMAGp971E141 109816 DNA helicase homolog PIF1

 ID No: IMAGp998L095608; IMAGp971N09128 2265368 Homo sapiens cDNA FLJ10417 fis, clone

NT2RP1000112

 ID No: IMAGp998E11660; IMAGp971E0330 295666

 ID No: IMAGp998K051891; IMAGp971K0650 768508 developmental pluripotency associated 4

 ID No: IMAGp998J14406; IMAGp971J1117 208621

 ID No: IMAGp998B231782; IMAGp971B2344 726454 sal-like 4 (Drosophila)

 ID No: IMAGp998M024021; IMAGp971P0165 1586473

 ID No: IMAGp998C105092; IMAGp971B0286 2067009

 ID No: IMAGp998I19131; IMAGp971E206 127962 Homo sapiens cDNA FLJ22539 fis, clone

 ID No: IMAGp998F246080; IMAGp971E22131 2445335 Homo sapiens mRNA for AND-1 protein

 ID No: IMAGp998B03791; IMAGp971F1134 345890 E2F transcription factor 1

 ID No: IMAGp998N15372; IMAGp971M1615 195662 cadherin 1, type 1, E-cadherin (epithelial)

 ID No: IMAGp998G201924; IMAGp971G2151 781099

 ID No: IMAGp998E1983; IMAGp971E212 109818

 ID No: IMAGp998C09200; IMAGp971D099 138176 hypothetical protein FLJ10652

 ID No: IMAGp998I204942; IMAGp971J2084 2009563

 ID No: IMAGp998H171818; IMAGp971I1747 740416 SRY (sex determining region Y)-box 17

 ID No: IMAGp998P175394; IMAGp971N18124 2183296 Homo sapiens cDNA FLJ12742 fis, clone

 ID No: IMAGp998F105821; IMAGp971B1898 2345865

 ID No: IMAGp998G01671; IMAGp971H0330 299928 Homo sapiens GN6ST mRNA for N-

acetylglucosamine-6-O-sulfotransferase (GlcNAc6ST)

 ID No: IMAGp998D125539; IMAGp971F1691 2238683

 ID No: IMAGp998C22571; IMAGp971D2123 261453

 ID No: IMAGp998M24260; IMAGp971I2312 161471 Sialyltransferase (CMP-N-

acetylneuraminate-beta-galactoside alpha- 2,6-sialyltransferase)

 ID No: IMAGp998N11579; IMAGp971K1823 264778 Solute carrier family 25 (mitochondrial

carrier; Graves disease autoantigen), member 16

 ID No: IMAGp998E15164; IMAGp971H10113 36807 Homo sapiens neutral sphingomyelinase

(N-SMase) activation associated factor

 ID No: IMAGp998N06288; IMAGp971L03118 52960 Homo sapiens, clone IMAGE4123507, mRNA

 ID No: IMAGp998M18194; IMAGp971N068 136121 Homo sapiens cDNA FLJ10247 fis, clone

HEMBB1000705

 ID No: IMAGp998J155722; IMAGp971K1295 2309102

 ID No: IMAGp998B21790; IMAGp971E1334 345524 integral membrane protein 2C

 ID No: IMAGp998J09792; IMAGp971C04134 346472 Homo sapiens, clone IMAGE4123507, mRNA

 ID No: IMAGp998H175550; IMAGp971H2092 2243008

 ID No: IMAGp998E24312; IMAGp971F2412 172415 Solute carrier family 35 (UDP-galactose

transporter), member A2

 ID No: IMAGp998J081153; IMAGp971J1040 485095 LOC388610 (LOC388610), mRNA

 ID No: IMAGp998G18196; IMAGp971H148 136745 hypothetical protein FLJ20171

 ID No: IMAGp998F241862; IMAGp971F2248 757271

 ID No: IMAGp998B09229; IMAGp971B0410 149288 Nedd4 family interacting protein 2

 ID No: IMAGp998E11127; IMAGp971H145 126322 Caspase 4, apoptosis-related cysteine

protease

 ID No: IMAGp998N02421; IMAGp971N0518 214465 Oxysterol binding protein-like 3

 ID No: IMAGp998B145536; IMAGp971B1592 2237485

 ID No: IMAGp998C144120; IMAGp971D1066 1624261

 ID No: IMAGp998M232973; IMAGp971E1958 1184062

 ID No: IMAGp998D051943; IMAGp971D0552 788308 Cell cycle progression 8 protein

 ID No: IMAGp998M031831; IMAGp971M0448 745514

 ID No: IMAGp998K243513; IMAGp971L2358 1391375

 ID No: IMAGp998B165468; IMAGp971J04132 2211375 Annexin A3

 ID No: IMAGp998G024171; IMAGp971L0469 1643929

 ID No: IMAGp998K15174; IMAGp971L16114 41539 Homo sapiens mRNA for KIAA0644 protein,

complete cds

 ID No: IMAGp998I04624; IMAGp971H0926 281931 cytoplasmic polyadenylation element

binding protein

 ID No: IMAGp998M24235; IMAGp971N2411 1518711 hypothetical protein FLJ22662

 ID No: IMAGp998F16280; IMAGp971H22117 49499 Dedicator of cytokinesis 11

 ID No: IMAGp998B23677; IMAGp971A2431 302134 H. sapiens mRNA for SOX-4 protein

 ID No: IMAGp998N204778; IMAGp971F1184 1946707 ESTs, Weakly similar to C Chain C, Human Activated Protein C

[H. sapiens]

 ID No: IMAGp998E163300; IMAGp971F12104 1309431

 ID No: IMAGp998P192044; IMAGp971O2055 827394 ash2 (absent, small, or homeotic)-like

(Drosophila)

 ID No: IMAGp998I144113; IMAGp971I1366 1621717 hypothetical protein LOC130576

 ID No: IMAGp998N045486; IMAGp971L02126 2218563

 ID No: IMAGp998I16328; IMAGp971J1413 178647 Myosin VA (heavy polypeptide 12, myoxin)

 ID No: IMAGp998C14658; IMAGp971A1330 294853 UDP-glucose ceramide glucosyltransferase

 ID No: IMAGp998M174328; IMAGp971I1573 1704376

 ID No: IMAGp998D065777; IMAGp971B0496 2328917 Vacuolar protein sorting 13A (yeast

 ID No: IMAGp998D01196; IMAGp971D199 136656 Sorting nexin 10

 ID No: IMAGp998B2070; IMAGp971A13110 22170 Homo sapiens family with sequence

similarity 16, member A, X-linked

 ID No: IMAGp998I17258; IMAGp971G1812 160600 Human mRNA for complement control

protein factor I

 ID No: IMAGp998M04179; IMAGp971M107 130347 Dysferlin, limb girdle muscular dystrophy

2B (autosomal recessive)

 ID No: IMAGp998K175764; IMAGp971N22120 2324104

 ID No: IMAGp998J11128; IMAGp971H045 126826

 ID No: IMAGp998H195650; IMAGp971K18129 2281410

 ID No: IMAGp998P025858; IMAGp971N0499 2360305

 ID No: IMAGp998M03208; IMAGp971N109 141482 Solute carrier family 38, member 1

 ID No: IMAGp998H07795; IMAGp971C0535 347574 Full length insert cDNA clone ZD86G04

 ID No: IMAGp998A112011; IMAGp971D15103 814354

 ID No: IMAGp998A205772; IMAGp971F2296 2326939 Timeless homolog (Drosophila)

 ID No: IMAGp998I09280; IMAGp971J02117 49203 DNA-damage-inducible transcript 4-like

 ID No: IMAGp998J24653; IMAGp971I1829 293111 Human cDNA for uracil-DNA glycosylase

 ID No: IMAGp998N161887; IMAGp971I2350 767055 Sema domain, immunoglobulin domain

(Ig), short basic domain, secreted, (semaphorin) 3A

 genes

 ID No: 134 THIOREDOXIN INTERACTING PROTEIN; UPREGULATED BY 1,25- DIHYDROXYVITAMIN D-3

 ID No: 135 CALDESMON (CDM).

 ID No: 136 HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, GAMMA CHAIN (HLA-DR ANTIGENS ASSOCIATED INVARIANT CHAIN) (IA ANTIGEN-ASSOCIATED INVARIANT CHAIN) (II) (P33) (CD74 ANTIGEN).

 ID No: 137 COMPLEMENT COMPONENT C7 PRECURSOR

 ID No: 138 SMALL INDUCIBLE CYTOKINE B16 (TRANSMEMBRANE CHEMOKINE CXCL16) (SR-PSOX) (SCAVENGER RECEPTOR FOR PHOSPHATIDYLSERINE AND OXIDIZED LOW DENSITY LIPOPROTEIN)

 ID No: 139 CYTOCHROME B REDUCTASE 1; DUODENAL CYTOCHROME B

 ID No: 140 INTERFERON-INDUCED TRANSMEMBRANE PROTEIN 1 (INTERFERON-INDUCED PROTEIN 17) (INTERFERON-INDUCIBLE PROTEIN 9-27) (LEU-13 ANTIGEN) (CD225 ANTIGEN).

 ID No: 141 SAL-LIKE PROTEIN 4 (ZINC FINGER PROTEIN SALL4).

 ID No: 142 ENDOPLASMIN PRECURSOR (94 KDA GLUCOSE-REGULATED PROTEIN) (GRP94) (GP96 HOMOLOG) (TUMOR REJECTION ANTIGEN 1).

 ID No: 143 ALPHA 2 TYPE I COLLAGEN; COLLAGEN I, ALPHA-2 POLYPEPTIDE; COLLAGEN OF SKIN, TENDON AND BONE, ALPHA-2 CHAIN

 ID No: 144 HISTONE DEACETYLASE 3 (HD3) (RPD3- 2).

 ID No: 145 HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN PRECURSOR

 ID No: 146 DYNAMIN-LIKE 120 KDA PROTEIN, MITOCHONDRIAL PRECURSOR (OPTIC ATROPHY 1 GENE PROTEIN).

 ID No: 147 BULLOUS PEMPHIGOID ANTIGEN 1 ISOFORMS 1/2/3/4/5/8 (230 KDA BULLOUS PEMPHIGOID ANTIGEN) (BPA) (HEMIDESMOSOMAL PLAQUE PROTEIN) (DYSTONIA MUSCULORUM PROTEIN)

 ID No: 148 DECORIN PRECURSOR (BONE PROTEOGLYCAN II) (PG-S2) (PG40)

 ID No: 149 LEUKOCYTE SURFACE ANTIGEN CD47 PRECURSOR (ANTIGENIC SURFACE DETERMINANT PROTEIN OA3) (INTEGRIN ASSOCIATED PROTEIN) (IAP) (MER6).

 ID No: 150 b2-microglobulin

 ID No: 151 60S RIBOSOMAL PROTEIN L27

 ID No: 152 40S RIBOSOMAL PROTEIN S16

 ID No: 153 UNCHARACTERIZED HYPOTHALAMUS PROTEIN HCDASE NM_018479

 ID No: 154 Overexpressed in CIS

 ID No: 155 Ensambl EST ENSESTT00000023592

 ID No: 156 Chromosome 16 clone

 ID No: 157 Chromosome-1 clone hypothetical protein XP_211586

 genes

 ID No: IMAGp998F065401; IMAGp971I06125 2185733 S100A14 S100 calcium binding protein A14

 ID No: IMAGp998J065499; IMAGp971I22120 2223461 transmembrane 4 superfamily member 3

 ID No: IMAGp998A05535; IMAGp971B0621 247564 Homo sapiens transcribed sequence with moderate

similarity to protein ref: NP_060190.1 (H. sapiens) hypothetical protein FLJ20234 [Homo

 ID No: IMAGp998B19790; IMAGp971B0934 345522 SEC13-like 1 (S. cerevisiae)

 ID No: IMAGp998M105514; IMAGp971K10120 2229297

 ID No: IMAGp998O095541; IMAGp971P0592 2239712 Homo sapiens transcribed sequence with weak similarity to

protein ref: NP_038602.1 (M. musculus) L1 repeat, Tf subfamily, member 18 [Mus musculus]

 ID No: IMAGp998D121896; IMAGp971D1150 770267

 ID No: IMAGp998H235725; IMAGp971H1195 2310214

 ID No: IMAGp998P03372; IMAGp971O0415 195698 Human fibrinogen beta chain gene,

complete mRNA

 ID No: IMAGp998B071870; IMAGp971C0749 760230 Homo sapiens secreted cement gland

protein XAG-2 homolog (hAG-2/R) mRNA, complete cds

 ID No: IMAGp998D08822; IMAGp971C0735 357847 coiled-coil domain containing 2

 ID No: IMAGp998I08822; IMAGP971C0635 357967 KIAA1712 protein

 ID No: IMAGp998D09822; IMAGp971C0935 357848 Homo sapiens similar to hypothetical protein

(LOC285177), mRNA

 ID No: IMAGp998K045001; IMAGp971H0285 2032251 chromosome 4 open reading frame 7

 ID No: IMAGp998K125400; IMAGp971C19125 2185475

 ID No: IMAGp998K151776; IMAGp971P2043 724358 keratin 19

 ID No: IMAGp998I164581; IMAGp971L1480 1870935 fibronectin 1

 ID No: IMAGp998F044825; IMAGp971I03121 1964547

 ID No: IMAGp998L206082; IMAGp971L19131 2446243

 ID No: IMAGp998D085368; IMAGp971A0792 2173015 Homo sapiens caudal-type homeobox gene

2 (CDX2) sequence

 ID No: IMAGp998D20611; IMAGp971E2025 276835 TPA regulated locus

 ID No: IMAGp998B14742; IMAGp971C2433 327085 discs, large (Drosophila) homolog-

associated protein 1

 ID No: IMAGp998B07407; IMAGp971E0417 208806 Human serum prealbumin gene, complete

cds

 ID No: IMAGp998C16522; IMAGp971C1521 242631 Human mRNA for apolipoprotein AII

precursor

 ID No: IMAGp998O055540; IMAGp971O0692 2239324 cholecystokinin B receptor

 ID No: IMAGp998A244944; IMAGp971B2484 2010143

 ID No: IMAGp998I15843; IMAGp971H1436 366038 SERUM ALBUMIN PRECURSOR

 ID No: IMAGp998K105256; IMAGp971F02120 2130177

 ID No: IMAGp998B094453; IMAGp971B2475 1752104

 ID No: IMAGp998G193982; IMAGp971E1864 1571370 Homo sapiens transcribed sequence with moderate similarity to

protein pir: S30392 (H. sapiens) S30392 phospholipase A2 homolog (clone AF-5) - human retrotransposon

 ID No: IMAGp998P194992; IMAGp971N1785 2028930 ESTs, Moderately similar to JE0065 retroviral proteinase-like

protein [H. sapiens]

 ID No: IMAGp998F015873; IMAGp971H0199 2365824

 ID No: IMAGp998A054888; IMAGp971B04121 1988620

 ID No: IMAGp998A04528; IMAGp971A0222 244875 Human cystathionine-beta-synthase (CBS)

mRNA

 ID No: IMAGp998H22207; IMAGp971I2210 140997 Growth differentiation factor 15

 ID No: IMAGp998P151066; IMAGp971M0340 451838

 ID No: IMAGp998K055550; IMAGp971D0892 2243068

 ID No: IMAGp998A065260; IMAGp971A0890 2131469 ETS2 v-ets erythroblastosis virus E26

oncogene homolog 2 (avian)

 ID No: IMAGp998J076121; IMAGp971M04102 2461158 Inhibitor of DNA binding 3, dominant

negative helix-loop-helix protein

 ID No: IMAGp998L10662; IMAGp971G0530 296601 H. sapiens mRNA for M130 antigen

cytoplasmic variant 2

 ID No: IMAGp998D0595; IMAGp971C043 114388

 ID No: IMAGp998G06783; IMAGp971L0333 342941 APLN apelin

 ID No: IMAGp998K08276; IMAGp971K12119 47615 Human MHC HLA-B7 class I cell surface

glycoprotein heavy chain mRNA, complete cds

 ID No: IMAGp998F152230; IMAGp971F1655 898574

 ID No: IMAGp998O075514; IMAGp971L03120 2229342 FLJ10808 hypothetical protein FLJ10808

na genes

 ID No: IMAGp998A022575; IMAGp971C0257 1030921

 ID No: IMAGp998E122300; IMAGp971F1455 925427

 ID No: IMAGp998C12278; IMAGp971H11117 48417 FRCP2 likely ortholog of mouse fibronectin

type III repeat containing protein 2

 ID No: IMAGp998E191782; IMAGp971A1744 726522 Homo sapiens similar to Envoplakin (210 kDa paraneoplastic

pemphigus antigen) (p210) (210 kDa cornified envelope precursor) (LOC339237), mRNA

 ID No: IMAGp998O124335; IMAGp971P1173 1707107 Human chitotriosidase precursor mRNA,

complete cds

 ID No: IMAGp998K102640; IMAGp971L1957 1056129

 ID No: IMAGp998F035711; IMAGp971E1095 2304770

 ID No: IMAGp998O184348; IMAGp971P2373 1712105 ALL1 fused gene from 5q31

 ID No: IMAGp998B201153; IMAGp971E1741 484915 RNA binding motif protein 5

 ID No: IMAGp998P08567; IMAGp971P0523 260215 Homo sapiens cDNA FLJ31733 fis, clone

NT2RI2006943

 ID No: IMAGp998A191006; IMAGp971B1539 428442 tachykinin 3 (neuromedin K, neurokinin

beta)

 ID No: IMAGp998B02152; IMAGp971I04112 31971 Human mRNA for KIAA0363 gene, partial

cds

 ID No: IMAGp998M23288; IMAGp971N21118 52650 Human erythroblastosis virus oncogene homolog 2 (ets-2)

 ID No: IMAGp998I12605; IMAGp971E1525 274643

 ID No: IMAGp998F015343; IMAGp971E0391 2163456 Chitinase 1 (chitotriosidase)

 ID No: IMAGp998B171824; IMAGp971E1447 742576 H. sapiens HE2 mRNA

 ID No: IMAGp998L24923; IMAGp971O2438 396839

 ID No: IMAGp998E135802; IMAGp971F1597 2338548 chitinase 1 (chitotriosidase)

 ID No: IMAGp998D171153; IMAGp971F2341 484960 hypothetical protein BC007899

 ID No: IMAGp998F17593; IMAGp971B1524 269968 Transcribed sequence with strong similarity to protein 1

pdb: 14GS (H. sapiens) B Chain B, Glutathione S- Transferase P1-1 Apo Form 1

 ID No: IMAGp998N11360; IMAGp971O1414 191050

 ID No: IMAGp998I152328; IMAGp971I2156 936278 Transcribed sequence with moderate similarity to protein

pir: S52491 (H. sapiens) S52491 polyadenylate binding protein II - human

 ID No: IMAGp998I112449; IMAGp971G05108 982738

 ID No: IMAGp998A17282; IMAGp971B18117 50008 Calcium channel, voltage-dependent, L

type, alpha 1B subunit

 ID No: IMAGp998J014173; IMAGp971J0469 1644768 Golgi autoantigen, golgin subfamily a,

member 6

 ID No: IMAGp998O235762; IMAGp971O22130 2323438

 ID No: IMAGp998C01743; IMAGp971D0132 327480 Collagen, type XXIII, alpha 1

 ID No: IMAGp998D175081; IMAGp971F1286 2062816 hypothetical protein LOC200213

 ID No: IMAGp998B2474; IMAGp971D23110 23877 ATPase, aminophospholipid transporter

(APLT), Class I, type 8A, member 1

 ID No: IMAGp998I094494; IMAGp971I0978 1837520 Homo sapiens transcribed sequence with moderate similarity to

protein pir: S52491 (H. sapiens) S52491 polyadenylate binding protein II - human

 ID No: IMAGp998B08733; IMAGp971A0333 323623 DKFZP564O1863 protein

 ID No: IMAGp998I11564; IMAGp971K1323 258898 Homo sapiens secreted frizzled-related

protein 2 (SFRP2), mRNA

 ID No: IMAGp998K211090; IMAGp971I2040 460940

 ID No: IMAGp998A181964; IMAGp971E0253 796313

 ID No: IMAGp998H04617; IMAGp971G0326 279219 chromosome 20 open reading frame 58

 ID No: IMAGp998I12670; IMAGp971L0430 299603

 ID No: IMAGp998D145711; IMAGp971D2194 2304733

 ID No: IMAGp998L06178; IMAGp971H02115 38015 Slit and trk like gene 2

 ID No: IMAGp998I135799; IMAGp971C2497 2337492 Hypothetical gene supported by AK126852

(LOC400516), mRNA

 ID No: IMAGp998D154762; IMAGp971D1183 1940318 disco-interacting protein 2 (Drosophila)

homolog

 ID No: IMAGp998P20366; IMAGp971O1915 193411 Human mRNA for alpha1-acid glycoprotein

(orosomucoid)

 ID No: IMAGp998C034512; IMAGp971C0279 1844282 transglutaminase 3 (E polypeptide,

protein-glutamine-gamma- glutamyltransferase)

 ID No: IMAGp998G01115; IMAGp971E01103 122136

 ID No: IMAGp998B22787; IMAGp971A2234 344373

 ID No: IMAGp998J134174; IMAGp971J1669 1645164 hypothetical protein LOC340094

 ID No: IMAGp998D04101; IMAGp971A034 116691

 ID No: IMAGp998D04101; IMAGp971A034 116691

 ID No: IMAGp998O0470; IMAGp971O03110 22040 Human type IV collagenase mRNA,

complete cds

 ID No: IMAGp998A125385; IMAGp971D14124 2179475 phospholipase A2, group IID

 ID No: IMAGp998D194160; IMAGp971F1767 1639650

 ID No: IMAGp998L132010; IMAGp971K1355 814236

 ID No: IMAGp998G081965; IMAGp971G1553 796831 Human metalloendopeptidase homolog

(PEX) mRNA, complete sequence

 ID No: IMAGp998B072455; IMAGp971B0956 984870 Similar to ankylosis, progressive homolog

50% 75% 100% Seminom/ Genename Chromosome CIS CIS CIS Seminoma EC EC

 ID No: NANOG 12p13.2 10.3 15.4 33.2

 ID No: hXBP1 2.0 30.0 25.5

 ID No: 23.8 14.7 24.6

 ID No: TMF1 24.8 27.6 16.6

 ID No: LIN28 1p35.3 3.6 4.7 15.0

 ID No: 11p15.4 10.1 14.0 15.0

 ID No: T1A-2 1p36 6.6 7.3 14.8

 ID No: 2.9 3.2 14.2

 ID No: 3.3 8.7 14.2

 ID No: 2.5 3.8 12.9

 ID No: SLC7A3 Xq12 2.6 2.1 12.3

 ID No: 14 6.7 4.5 11.4

 ID No:  6 NA 2.7 10.0

 ID No: 1p32.1 2.3 3.7 10.0

 ID No: 19.4 16.4 9.9

 ID No:  7 NA 5.8 9.1

 ID No: 2.9 4.8 9.0

 ID No: 1p35.3 3.8 3.8 8.6

 ID No: SCGB3A2 5q32 2.7 5.2 8.3

 ID No: TFAP2C 20q13.2 2.4 3.8 8.2

 ID No: EFEMP1 2p16 5.6 3.1 8.2

 ID No: NFE2L3 7p15-p14 3.5 6.1 8.1

 ID No: PIM2 Xp11.23 2.5 2.5 8.0

 ID No:  2 2.9 2.9 8.0

 ID No: MYBL2 2.7 2.8 7.7

 ID No: GLDC 9p22 2.8 3.7 7.5

 ID No: LBP-9 2q14 2.8 3.2 7.4

 ID No: RAB15 14 3.4 4.3 7.4

 ID No: ALPL 1p36.1-p34 1.9 2.4 7.3

 ID No: 5.1 3.7 7.3

 ID No: PRDM1  6 6.0 6.4 7.1

 ID No: UP 2.3 3.3 7.1

 ID No: 1.5 3.0 6.9

 ID No: 2.0 6.9 6.7

 ID No: TFCP2L1 2.5 4.9 6.7

 ID No: 2.5 3.5 6.6

 ID No: 2.4 4.3 6.4

 ID No: HLXB9 1.7 3.1 6.3

 ID No: PHLDA3 1q31 3.1 2.7 6.2

 ID No: 2.2 3.1 6.1

 ID No: COL22A1 2.0 3.3 6.1

 ID No: NALP9 1.3 4.3 6.1

 ID No: 2.4 3.5 6.0

 ID No:  1 6.0 5.9 6.0

 ID No: TEAD4 12p13.2-p13.3 2.0 2.8 5.9

 ID No: TCL1B, 14q32.1 1.7 4.0 5.9

TCL6

 ID No: ETV4 17q21 3.8 3.1 5.8

 ID No: DKFZP76 1p36.13 2.2 3.3 5.7

2N0610

 ID No: 2.1 2.8 5.6

 ID No: 2.3 3.0 5.5

 ID No: LRP4 11p11.2-p12 4.2 4.5 5.5

 ID No: TCL1A 14q32.1 2.7 3.1 5.5

 ID No: PROCR 20 14.1 7.6 5.4

 ID No: 1.3 2.3 5.3

 ID No: LCE 4q25 NA 5.2 5.3

 ID No: 1.8 3.7 5.3

 ID No: ETV5 3q28 2.1 2.8 5.3

 ID No:  1 1.9 2.8 5.2

 ID No: PIF1 15q22.1 1.9 2.5 5.1

 ID No:  7 2.0 4.7 5.1

 ID No: 3.2 4.0 5.1

 ID No: DPPA4 1.2 2.4 4.9

 ID No: E2IG2 2.5 2.1 4.8

 ID No: SALL4 20q13.13-q13.2 2.1 2.8 4.8

 ID No: 1.9 2.6 4.8

 ID No: 2.2 2.2 4.7

 ID No: HRC13227  4 2.2 3.2 4.7

 ID No: AND-1 14q22.1 0.9 2.1 4.7

 ID No: E2F1 4.6 2.8 4.7

 ID No: CDH1 16q22.1 1.7 2.1 4.7

 ID No: 2.2 2.6 4.6

 ID No: 2.1 2.3 4.5

 ID No: FLJ10652 12p12.1 2.3 3.5 4.5

 ID No: 2.1 2.5 4.4

 ID No: SOX17 8q11.22 2.0 2.2 4.4

 ID No: NT2RP2000644 NA 10.5 4.3

 ID No: 2.3 3.7 4.4

 ID No: CHST2 3q24 2.8 2.1 4.2

 ID No: 1.4 2.5 4.2

 ID No: 1.8 2.4 4.1

 ID No: SIAT1 3q27-q28 2.7 3.0 4.1

 ID No: SLC25A16 10q21.3-q22.1 1.6 2.3 4.1

 ID No: NSMAF 2.4 3.7 4.0

 ID No: 2.0 2.8 4.0

 ID No: 14 4.8 2.4 4.0

 ID No: 2.6 2.4 4.0

 ID No: ITM2C 2q37 2.8 2.3 4.0

 ID No: 2.2 2.9 3.9

 ID No:  3 2.1 2.2 3.9

 ID No: SLC35A2 Xp11.23-p11.22 2.1 2.6 3.9

 ID No: 2.2 2.2 3.8

 ID No: FLJ20171 8q21.3 3.2 2.4 3.8

 ID No: 2.5 2.8 3.8

 ID No: NDFIP2 13q22.2 5.7 4.9 3.7

 ID No: CASP4 5.1 2.6 3.7

 ID No: OSBPL3 7p15 4.2 4.0 3.6

 ID No: 1.1 2.2 3.6

 ID No: 1.5 2.7 3.6

 ID No: 2.5 3.2 3.6

 ID No: CPR8 15q21.1 2.0 2.2 3.6

 ID No: 4.1 3.3 3.5

 ID No: 1.3 3.3 3.5

 ID No: ANXA3 4q13-q22 2.6 2.7 3.5

 ID No: 1.4 4.0 3.5

 ID No: KIAA0644 7p21.1 1.8 3.6 3.4

 ID No: CPEB1 15q24.2 1.4 2.6 3.4

 ID No: FLJ22662 12p13.31 2.6 2.2 3.4

 ID No: DOCK11 2.3 2.8 3.4

 ID No: SOX4 6p23 2.0 2.4 3.4

 ID No: 2.5 3.4 3.4

 ID No: 2.4 2.9 3.3

 ID No: ASH2L 2.3 2.6 3.3

 ID No: 0.6 3.5 3.3

 ID No: 1.4 2.2 3.3

 ID No: MYO5A 15 2.1 2.0 3.3

 ID No: UGCG  9 1.8 2.5 3.2

 ID No: 2.2 2.5 3.2

 ID No: VPS13A 2.0 2.7 3.2

 ID No: SNX10 7p21.1 1.6 4.9 3.2

 ID No: FAM16AX Xp22.32 2.0 2.1 3.2

 ID No: IF 4q25 6.5 2.3 3.2

 ID No: DYSF 2p13.3-p13.1 2.9 2.3 3.2

 ID No: 1.8 2.8 3.2

 ID No: 0.8 2.7 3.2

 ID No: 1.3 2.3 3.1

 ID No: 1.5 2.6 3.1

 ID No: SLC38A1 1.9 2.5 3.1

 ID No: 2.1 2.6 3.1

 ID No: 1.3 2.9 3.1

 ID No: TIMELESS 1.5 2.1 3.1

 ID No: DDIT4L 4q23 2.9 5.5 3.1

 ID No: UNG 12 1.8 2.7 3.0

 ID No: SEMA3A 1.9 2.3 3.0

 genes

 ID No: 134 TXNIP

 ID No: 135 CALD1

 ID No: 136 CD74

 ID No: 137 C7

 ID No: 138 CXCL16

 ID No: 139 CYBRD1

 ID No: 140 FITM 1

 ID No: 141 SALL4

 ID No: 142 TRA1

 ID No: 143 COL1A2

 ID No: 144 HDAC3

 ID No: 145 HLA-DRA

 ID No: 146 OPA1

 ID No: 147 BPAG1

 ID No: 148 DCN

 ID No: 149 CD47

 ID No: 150

 ID No: 151 RPL27

 ID No: 152 RPS16

 ID No: 153

 ID No: 154 OIC1

 ID No: 155

 ID No: 156

 ID No: 157

 genes

 ID No: S100A14 1.1575 1.335 1.685 0.6 24.36 0.105

 ID No: TM4SF3 3.165 0.88 0.9625 0.6 17.62 0.05

 ID No: 10 1.1025 1.15 1.4575 1.29 15.53 NA

 ID No: 2.3325 0.845 0.5625 0.61 15.035 0.065

 ID No: 2.3675 0.87 0.5475 0.715 14.865 0.085

 ID No: 1.21 1.23 0.95 0.93 13.86 0.06

 ID No: 0.79 0.705 0.5075 0.695 13.475 0.04

 ID No: 0.8525 0.61 0.835 1.05 13.38 0.06

 ID No: FGB 4q28 1.205 1.36 1.105 0.8 11.695 0.08

 ID No: AGR2 7p21.3 0.78 0.725 0.71 1.2 11.05 0.06

 ID No: CCDC2 2.14 0.85 0.56 0.67 9.57 0.105

 ID No: KIAA1712 2.145 0.865 0.58 0.89 9.5 0.065

 ID No: FLJ20958 1.955 0.875 0.605 0.655 9.415 0.095

 ID No: C4orf7 0.795 1.015 1.055 1.405 9.35 0.095

 ID No: 0.665 0.82 1.165 1.02 9.3 0.08

 ID No: KRT19 15 0.88 0.91 0.77 0.56 8.88 0.065

 ID No: FN1 1.7425 0.8 0.685 0.755 8.875 0.09

 ID No: 0.8275 1.325 0.955 0.915 8.615 0.105

 ID No: 0.8725 0.79 0.9425 1.185 8.475 0.15

 ID No: CDX2 13q12.3 1.185 0.97 0.985 1.34 8.415 0.165

 ID No: TPARL 4q12 1.06 1.46 0.8625 1.125 8.395 0.1

 ID No: DLGAP1  8 2.6125 0.98 0.755 0.695 7.83 0.095

 ID No: TTR 18q12.1 0.8325 0.965 0.95 0.925 7.675 0.175

 ID No: APOA2 1q21-q23 0.615 0.85 1.065 1.12 7.51 0.28

 ID No: CCKBR 1.115 0.855 1.45 0.995 7.25 0.11

 ID No: 0.85 1.15 1.785 1.21 7.175 0.12

 ID No: Q8IUK7 0.64 1.28 1.01 0.86 7.01 0.24

 ID No: 0.56 0.88 0.8925 0.79 6.835 0.31

 ID No: 1.2275 0.855 0.77 0.63 6.765 0.26

 ID No: 1.2325 1.335 1.49 1.82 6.69 0.11

 ID No: 1.4825 1.23 1.7875 1.33 6.685 0.15

 ID No: 3.56 1.845 0.87 1.83 6.505 0.305

 ID No: 1.5625 0.88 1.02 0.925 6.45 0.125

 ID No: CBS 21q22.3 1.3275 0.925 0.795 1.735 6.33 0.085

 ID No: GDF15 19p13.1-13.2 1.095 1.18 1.0975 1.515 6.23 0.14

 ID No: 2.61 1.385 0.7125 0.915 5.995 0.115

 ID No:  2 1.825 2.145 1.45 1.49 5.965 0.27

 ID No: ETS2 3.2925 1.38 1.58 0.695 5.965 0.22

 ID No: ID3 1.7475 0.93 1.0025 0.85 5.85 0.13

 ID No: CD163 12p13.3 4.7225 1.315 0.565 1.79 5.77 0.115

 ID No: 3.07 2.04 1.7 0.775 5.765 0.165

 ID No: APLN Xq25-26.3 1.4975 3.02 1.8725 0.905 5.75 0.13

 ID No: HLA-B 6p21.3 NA 1.735 0.74 1.925 5.71 0.27

 ID No: 1.545 0.95 1.065 1.68 5.7 0.15

 ID No: FLJ10808 3.1825 2.86 1.83 0.515 5.69 0.155

na genes

 ID No: 0.755 1.165 0.81 5.92 0.59 19.32

 ID No: 0.765 1.1 0.8375 7.37 0.47 11.74

 ID No: FRCP2 1.4325 1.48 3.045 3.135 0.135 10.505

 ID No: 0.975 1.125 0.8925 5.3 0.895 7.96

 ID No: CHIT1 1q31-q32 1.4275 1.065 0.82 13.945 0.92 7.67

 ID No: 1.05 0.68 1.265 5.195 0.17 7.165

 ID No: 1.51 1.23 1.85 8.875 0.705 5.34

 ID No: AF5Q31 5q31 0.9475 0.795 0.97 6.575 0.585 4.925

 ID No: RBM5 3p21.3 1.4275 1.15 1.485 4.95 0.92 4.665

 ID No: 12 0.9425 0.955 1.2775 3.575 0.68 4.6

 ID No: TAC3 12q13-q21 0.6375 1.045 0.8875 7.06 0.45 4.41

 ID No: KIAA0363 7p15.1 1.5125 1.515 1.78 3.735 0.32 4.3

 ID No: 0.365 0.635 0.3925 3.1 0.335 4.14

 ID No: NA NA NA 4.11 0.41 4.115

 ID No: CHIT1 0.85 1.205 0.9575 4.56 0.675 3.98

 ID No: SPAG11  8 1.005 1.11 0.855 3.635 1.78 3.9

 ID No: 13 1.1 0.845 0.7575 3.235 0.5 3.89

 ID No: CHIT1 1.165 1.05 1.015 3.89 0.935 3.65

 ID No: LOC148898 1p36.11 0.5775 0.765 0.55 4.18 1.28 3.595

 ID No: 1.495 1.645 4.11 5.04 0.51 3.49

 ID No: 0.89 0.95 0.9675 6.375 0.77 3.47

 ID No: 0.525 0.76 0.7275 3.06 0.37 3.425

 ID No: 1.74 1.31 0.855 5.835 0.97 3.3

 ID No: CACNA1B  9 1.1675 1.35 1.155 3.475 0.6 3.285

 ID No: GOLGA6 3.2825 1.34 0.91 12.645 1.23 3.26

 ID No: 0.875 1.355 1.1025 3.445 0.465 3.24

 ID No: COL23A1  5 1.195 1.345 1.61 3.25 0.495 3.05

 ID No: LOC200213 1.4125 1.425 1.7625 3.165 0.48 3.025

 ID No: ATP8A1  4 2.2925 1.815 1.565 3.275 0.58 3.015

 ID No: 0.6 0.89 0.7725 3.37 0.28 3.005

 ID No: DKFZP564O1863 12p12.3 1.155 1.335 0.95 5.315 1.005 2.985

 ID No: SFRP2 1.9175 1.6 1.4625 5.425 0.595 2.86

 ID No: 0.865 1.26 1.445 5.265 0.545 2.86

 ID No: 1.41 1.25 3.07 4.805 1.27 2.85

 ID No: C20orf58 20 1.2025 1.075 1.0825 3.935 0.495 2.845

 ID No: 1.35 2.66 1.9625 4.195 1.03 2.81

 ID No: 1.045 0.615 1.2575 4.38 1.46 2.78

 ID No: SLITRK2 1.055 1.42 1.2175 4.23 0.615 2.78

 ID No: 1.905 0.87 0.76 3.9 0.995 2.645

 ID No: DIP2 21q22.3 1.0925 1.245 1.325 3.34 0.65 2.52

 ID No: ORM1, ORM2 9q31-q32 0.865 0.81 1 4.54 0.675 2.435

 ID No: TGM3 0.69 1.465 0.54 3.72 0.705 2.415

 ID No:  2 0.7625 1.05 1.045 4.26 0.51 2.315

 ID No:  9 0.5275 0.99 2.345 5.42 0.505 2.305

 ID No: 1.265 0.94 0.7825 4.99 0.93 2.26

 ID No: 1.05 1.035 1.165 6.91 0.79 2.23

 ID No: 1.05 1.035 1.165 6.91 0.79 2.23

 ID No: MMP9 20q11.2-q13.1 1.0825 1.05 0.9175 6.705 2.12 2.095

 ID No: PLA2G2D 1p36.12 1.355 1.02 0.8925 4.54 1.095 2.05

 ID No: 1.485 1.225 1.395 3.85 0.62 2.03

 ID No: 0.635 1.06 0.685 4.8 0.735 2.025

 ID No: PHEX Xp22.2-p22.1 1.4175 1.31 1.135 3.235 0.74 2

 ID No: 1.3475 1.025 0.99 85.23 1.39 1.12

indicates data missing or illegible when filed

lists features descriptions of all the sequences. In most instnaces the RZPD (German Resource Center for Genome Research) and

clone numbers are reported. In addition to that, also the best applicable feature description and gene name as well as chromosomal

is reported. In the last 6 columns results from the microarray study are reported. 50%, 75%, and 100% CIS reflects analysis on

with CIS in 50%, 75, and 100% of the tubules in a given sample. Seminoma reflects a sample with classical seminoma and EC

a sample with embryonal carcinoma. Seminoma/EC reflects an individual experiment with seminoma vs. EC.

and evaluation of the results of the AP-2γ staining of semen samples from the various patient categories. The staining was classified using an arbitrary

after a systematical and independent evaluation by two investigators (CHH and ERM), who had no prior knowledge of the diagnosis. The group with

neoplasms included patients with the following tumours: 5 seminomas, 4 non-seminomas, 1 mixed GCT and 2 unilateral CIS, which had not proceeded

tumour, and the subfertile patient diagnosed with CIS in this study. The group of patients with other diseases comprised: 1 benign testis tumour

adenoma), 1 malignant lymphoma, 2 Hodgkin's disease, 1 glioblastoma, 1 Wegeners granulomatosis, 1 Crohn's disease, 1 bone tumour, 1 torsio testis,

tumour, 1 Klinefelter, 1 XYY male. The healthy controls were recruited among apparently healthy young men attending our department for other

and 59 subfertile men, of whom 16 had normospermia and 43 had oligospermia. Statistical analysis of data were performed using the Confidence Interval

programme, version 2.0, developed by D.G. Altman, D. Machin, T.N. Bryant and M.J. Gardner.

TABLE II Mean age AP-2γ-positive Studied groups N (years) N (%, 95% CI) Testicular tumour or CIS before  13^(#) 33  6^(#) (46.2%, CI 23-71%)   operation/irradiation Testicular cancer after operation,  7 32 0 (0%, CI 0-35%)

 contralateral CIS Other diseases 12 29 0 (0%, CI 0-24%) Healthy controls 14 32 0 (0%, CI 0-22%) subfertile patients with normospermia 16 32 0 (0%, CI 0-19%) subfertile patients with oligospermia  43^(#) 34  1^(#) (2.3%, CI 0.4-12%)

indicates data missing or illegible when filed

TABLE III Summary of the Immunohistochemical staining for AP-2γ. AP-2γ (staining intensity and approximate % of

N Histology/Diagnosis positive cells in a section) Remarks

 testes: 10.22 wg 11 Normal fetal testes − to ++ (75-100%) 3 samples negative

 wg 4 Normal fetal testes +/− to + (5-50%)

 wg 2 Normal fetal testes +/− (<10%)

 months 2 Normal infantile testes − to + (25%)

 months 5 Normal infantile testes +/− (single cells or <10%)

 years 3 Normal infantile testes −

 years 7 Normal pre-pubertal testes −

 years 1 Normal testes with complete spermatogenesis −

 ovaries:

1 Normal fetal ovary + (single cells) Oogonia+

 wg 5 Normal fetal ovaries +/− to + Oogonia+, oocytes−

 wg 7 Normal fetal ovaries +/− to ++ Oogonia+, oocytes−

 wg 9 Normal fetal ovaries + to ++ Oogonia+, oocytes−

1 Normal adult ovary −

 and intersex gonads:

 wg 1 Fetal testis (mosaic isochromosomeY) − AMH+, Oct4-

2 Fetal testes (AIS, 46, XY females) + (10%)

 months 1 Infantile testis (AIS, 46, XY females) + (5%)

 months 1 Ovotestis (46 XX hermaphrodite) +/− Gonocytes positive, oocytes negative

 months - 6 3 Pre-pubertal testes (AIS, 46 XY females) + to +++ (2-10%) Gonocytes with CIS

characteristics, PLAP+ or −.

6 Pre-pubertal testes (AIS, 46 XY females) −

 years 1 Infantile testis with decreased number of germ − cell (idiopathic genital ambiguity)

 years 1 Pre-pubertal testis (Prader-Willy's syndrome) −

 years 1 Leydig-cell hyperplasia (adrenogenital − syndrome)

 years 1 46, XY female, 17βHD mutation −

 years 1 Dysgenetic testis with CIS and gonadoblastoma ++ (90-100%) (45, X/46XY male)

 years 1 Klinefelter, bilateral testicular cryptorchidism −

 years 9 Adult testes with TDS (undifferentiated tubules, − microliths) but without CIS or TGCT

 years 3 Adult testes with TDS (undifferentiated tubules, − microliths) and contralateral TGCT

 carcinoma in situ and tumour samples:

5 CIS adjacent to seminomas + to +++ (90-100%)

5 CIS adjacent to non-seminomas + to +++ (90-100%)

2 CIS adjacent to mixed TGCT ++ (90-100%)

2 CIS without overt TGCT +++ (90-100%)

12 Classical, homogenous seminomas + to +++ (90-100%)

12 Non-seminomas +/− to ++ Various epithelial and stromal elements positive

2 Spermatocytic seminomas −

/6 years 3 Leydig cell tumors − to + Cytoplasmic, background?

 years 1 Gonadoblastoma +++

1 Testicular B-cell lymphoma −

issue samples:

1 of Liver, heart, thymus, thyroid gland, kidney and −

 wg each adrenal gland

11 Normal breast tissues + to ++ (90-100%) Subpopulation of basally situated duct cells

47 Infiltrating ductal breast adenocarcinomas 7 samples +/− (<10%) 7 samples + (50%) 33 samples −

1 Breast mucinous carcinoma −

4 Breast medullary carcinomas 2 samples +/− (90-100%)

3 Ductal breast carcinoma in situ +/− Single basal cells

2 Tubular breast cancers −

1 Infiltrating nodular breast adenocarcinoma −

4 Lung + Epithelial pneumocytes positive

7 Skin +/− (25%) Basal cells

1 Kidney +/− (50%) Single cells in canaliculi, glomeruli−

1-3 Skeletal muscle, heart muscle, stomach, − of esophagus, small intestine, colon, liver, spleen, each pancreas, salivary gland, pituitary gland, adrenal gland, thyroid gland, parathyroid gland, thymus gland, tonsil, epididymis, uterus, cervix, ovarian serous adenocarcinoma, prostate gland, prostatic cancer, omentum, peripheral nerve, cerebral cortex, cerebellum

ll lines

 cells Day 0, 3, 15 of retinoic acid treatment − to + In all samples a subpopulation of cells were stained.

Day 0, 1, 3, 7, 10 of retinoic acid treatment ++ In all samples most cells were stained.

Exposed to ICI-182, 780, ethanol or 1 nM − to + In all samples a estradiol for 24 or 48 h. subpopulation of cells were stained. Abbreviations: N = number; wg = weeks of gestation; AIS = androgen insensitivity syndrome; AMH = anti-Müllerian hormone; TDS = testicular dysgenesis syndrome; TGCT = germ cell tumor; CIS = carcinoma in situ. Staining intensity: +++: strong staining, ++: moderate staining, +: weak staining, +/−: very weak staining, −: no positive cells detected.

indicates data missing or illegible when filed

EXAMPLES Materials and Methods Tissue Samples

The testicular tissue samples were obtained directly after orchidectomy and macroscopic pathological evaluation. The use of the orchidectomy samples was approved by the Regional Committee for Medical Research Ethics in Denmark. Samples of homogeneous overt tumors (seminoma or EC) and of testicular parenchyma preserved in the vicinity of a tumor were excised. Each testicular sample was divided into several tissue fragments: 2-3 fragments were snap-frozen at −80° C. for nucleic acid extraction, several adjacent fragments were fixed overnight at 4° C. in Stieve's fluid or paraformaldehyde (PFA), and embedded in paraffin. Fixed sections were subsequently stained with haematoxylin and eosin (HE) or with an antibody against PLAP for histological evaluation. Most samples of testicular parenchyma contained variable numbers of tubules with CIS cells. Samples where no tubules with CIS were found and complete spermatogenesis was present, were used as a normal reference. In an attempt to limit the uncertainty about cellular differences between fragments from the same patient, the present inventors also made a direct print of the frozen fragment that specifically was used for RNA isolation. After staining with a PLAP antibody, the present inventors could roughly confirm the approximate proportion of tubules with CIS as established by histology in adjacent tissue fragments. Samples of tissue containing approximately 50%, 75%, and 100% tubules with CIS cells were chosen for microarray analysis along with the above-mentioned samples of overt tumours and the normal testicular tissue (serving as the common reference). Additional samples of teratomas and embryonal carcinomas were also used in the differential display screening and in the RT-PCR.

Labeling of Testicular RNA and Hybridization to Microarrays

Total RNA was purified using the Macherey & Nagel kit, DNase digested, and the RNA quality evaluated using the Agilent Bioanalyzer 2100 (Agilent Technologies Inc., CA, USA), 5 μg of total RNA was linearly amplified using the RiboAmp RNA amplification kit (Arcturus GmbH, Germany) yielding a 400-700 fold amplification of the mRNA. The amplified mRNA was reevaluated on the Bioanalyzer 2100 and 5 μg was then subjected to in-direct labeling with Cy3 and Cy5 (Amersham Biosciences) using the Atlas Glass Fluorescent labeling kit (3D Biosciences Clonetech, CA, USA).

The labeled RNA probes were combined and hybridized at 42° C. over night to a 52.000 element cDNA microarray representing the complete Unigene database. The microarray consists of two slides, which are hybridized on top of each other with the labeled probe inbetween. Production and handling of the microarray is described elsewhere (http://emblh3r.embl.de/). Hybridized slides were washed at 42° C. for 5 min in 2×SSC, 0.1% SDS and 10 min in 0.2×SSC, 0.1% SDS, rinsed, dipped in isopropanol, and dried.

Slides were scanned on a GenePix 4000B scanner (Axon Instruments Inc., Union City, Calif., USA) using settings where overall intensity of each channel was equal. The generated images were then analyzed in ChipSkipper (http://chipskipper.embl.de/) and quantified using a histogram segmentation. Flagged spots and controls were taken out and quantified spots were normalized using a framed median ratio centering (frame=200 genes). The average of dye-swaps was used and spots that did not dye-swap or showed a big standard deviation were sorted out. Data was then imported into software Genesis where hierarchical clustering was done using average linkage and Euclidian distances.

Differential Display Competitive PCR Screening

Total RNA was prepared using the RNeasy kit from Qiagen as described by the manufacturer (Qiagen, Hilden, Germany). RNA samples were double DNAse digested, first “on-column” and subsequently after the RNA had been purified. cDNA was prepared using one-base-anchored AAGCT11V (V=A, C or G) downstream primers. DDRT-PCR (Liang and Pardee, 1992) was subsequently performed using either one- or two-base-anchored (AAGCT11VN; N=A, C, G or T) primers in combination with different of upstream primers. Bands of interest were cut from the DDRT-PCR gels and reamplified using the up- and downstream primers that displayed the bands, but the downstream primer was extended at the 5′-end with a T7-promotor sequence (taatacgactcactatagggAAGCT11V; T7 promotor sequence in small letters), allowing direct sequencing on ALFexpress sequencers (Amersham-Pharmacia Biotech, Uppsala, Sweden), using a Cy5-labelled T7-promotor complementary primer. The DDRT-PCR method has been described in detail previously (Jorgensen, M, et al. Electrophoresis 1999, 20:230-40).

Verification by RT-PCR

The expression of a selected set of the regulated genes identified in the microarray analysts was verified with RT-PCR as described previously. In brief, cDNA was synthesized using a

primer. Specific primers targeting each mRNA were designed spanning

(final concentrations): 12 mM Tris-HCl, pH 8.3; 50 mM KCl; 1.9 mM MgCl2; 0.1% Triton X-100; 0.005% Gelatine; 250 μM dNTP; and 30 pmol of each primer. H2O was used as a negative control and β-actin was used as an internal control in all PCR reactions, resulting in an approximately 800 base pair actin fragment. Cycle conditions: 1 cycle of 2 min. at 95° C.; 30-40 cycles (depending on the intensity of bands) of: 30 sec. at 95° C., 1 min. at 62° C., 1 min. at 72° C. and finally 1 cycle of 5 min. at 72° C. PCR products were resolved on 1.5% agarose gels and visualized by ethidium bromide staining. Digital images of the agarose gels were quantified by the STORM phosphor imager software (ImageQuant, Amersham Biosciences). In a few of the RT-PCR analyses of less abundant transcripts, no bands were detectable after PCR and nested primers were designed. One μl from the first PCR reaction was transferred to a new reaction containing the nested primers and analyzed as above.

Preparation of Biotin-Labeled Probes and In Situ Hybridization

In situ hybridization was performed to confirm that the identified transcripts were indeed expressed in CIS cells. Probes for in situ hybridization were prepared by re-amplification of the PCR products using nested primers specific to the individual products and with an added T7- or T3-promotor sequence. PCR conditions were: 5 min. 95° C.; 5 cycles of: 30 sec. 95° C., 1 min. 45° C., 1 min. 72° C.; 20 cycles of 30 sec. 95° C., 1 min. 65° C., 1 min. 72° C. and finally 5 min. 72° C. The resulting PCR product was purified on a 2% low melting point agarose gel and sequenced from both ends, using Cy5-labelled primers complementary to the added T3 and T7 tags. Aliquots of about 200 ng were used for in vitro transcription labeling, using the MEGAscript-T3 (sense) or MEGAscript-T7 (anti-sense) kits, as described by the manufacturer (Ambion, Houston, Tex., USA). The composition of the 10×-nucleotide mix was: 7.5 mM ATP, GTP and CTP, 3.75 mM UTP, 1.5 mM biotin-labeled UTP. To estimate quantity and labeling efficiencies, aliquots of the labeled RNA product were analyzed by agarose gel electrophoresis, and dotted onto nitrocellulose filters and developed as described below.

In situ hybridization was performed essentially as described previously (Nielsen, J E, et al. Eur J Histochem 2003, 47:215-22), except for one additional step needed to remove mercury from sections fixed in Stieve fixative. After deparaffination, mercury was removed by 15 min. treatment with potassium iodide (KI/I ratio 2/1), followed by three washes in DEPC water. The iodine was subsequently removed by incubation in sodium thiosulfate pentahydrate (5% w/v, 10 min.) followed by washing (4× DEPC water). Subsequently, the procedure was, in brief, as follows: sections were re-fixed in 4% PFA, treated with, proteinase K (Sigma, St. Louis Mo. USA) (1.0-5.0 μg/ml), post-fixed in PFA, pre-hybridized

Visualization was performed with streptavidin conjugated with alkaline phosphatase (1:1000) (Roche Diagnostics GmbH, Mannheim, Germany) followed by a development with BCIP/NBT (Nielsen, J E, et al. Eur J Histochem 2003, 47:215-22).

Example 1 Genes Identified by Microarray

By analyzing testicular samples containing increasing amounts of tubules with CIS the present inventors identified differentially expressed genes as compared to the normal reference with complete spermatogenesis and no CIS cells present.

From normalized scatter plots of gene expression in CIS-containing-tissue versus normal testis tissue, the present inventors observed that approximately 200-300 genes were significantly up-regulated in CIS-containing tissues. Data was filtered so that only genes that were up-regulated in the CIS samples and had low standard deviation were considered for further analysis. The up-regulated genes were a heterogeneous group including transcription factors, such as TFAP2C (ERF-1), LBP-9, TEAD4 (RTEF-1), NFE2L3 (NRF3) and POU5F1, solute carriers e.g. SLC25A16, SLC7A3, oncogenes e.g. RAB-15, TCL1B (TML1), MYBL2 (B-MYB), PIM2 and many more genes, which are listed in Table X. Some of these genes were previously described as CIS markers, e.g. KIT (c-KIT), POV1 (PB39), MYCN (N-MYC) and POU5F1 (OCT-3/4), but the majority were novel, not previously characterized genes.

A hierarchical cluster analysis with average linkage of the top most up-regulated genes (minimum 4 fold increase in the sample with CIS in 100% of the tubules and more than 2 fold in the other samples) is shown in FIG. 1. For most of the genes, a gradual increase in expression was observed with increase in the percent of tubules with CIS. This strongly indicates that expression of these genes is linked to the CIS phenotype and indeed to the actual amount of tubules with CIS in the testis. To verify that, the present inventors reanalyzed the expression of selected genes by RT-PCR, in a panel of samples covering a broad spectrum of different testicular neoplasms and normal testicular tissue (FIG. 2A). We also investigated the expression of the non-tissue specific alkaline phosphatase (ALPL) simultaneously with the previously known CIS marker PLAP and found that they were expressed in a similar manner (FIG. 2A).

Both the microarray and the RT-PCR analysis indicated that the observed up-regulation of genes in the samples with CIS were linked to the CIS phenotype and thus to CIS cells.

TCL1A, TCL1B), may be due to the presence of infiltrating lymphocytes, which are commonly seen in patients with CIS, but not present in the normal testis (Jahnukainen, K, et al. Int J Androl 1995, 18:313-20). In addition, some transcripts up-regulated in the tissues with CIS may originate from immature Sertoli cells, which are sometimes present in testes with CIS, but such dysgenetic changes are relatively rare, so this possibility is less likely.

To confirm the cellular localization, the present inventors performed in situ hybridization for some of the identified genes on tissue sections with CIS. All transcripts tested (NANOG, ALPL, TFAP2C, and SLC7A3) were localized to CIS cells. The present inventors also observed in some cases variable staining of Sertoli cell nuclei, which was most probably unspecific, since similar, but lighter staining was observed for the control sense probe. However, in all cases, the strongest signal was from CIS cells.

Example 2 Genes Identified by Differential Display

To obtain knowledge on gene expression changes between the different stages in the development from non-malignant testicular tissue through CIS to the malignant stage of a germ cell cancer, the present inventors performed a systematic comparison by the DDRT-PCR method (Jorgensen, M, et al. Electrophoresis 1999, 20:230-40). For the initial screening the present inventors analysed six testicular biopsy samples: two with homogenous classical seminoma, two containing almost exclusively CIS tubules, of which one was from an intraabdominal CIS and two with normal spermatogenesis. The undescended testis with CIS was of our interest, because in the hypothesis of Testicular Dysgenesis Syndrome, both testicular cancer and undescended testes are symptoms of maldeveloped genitalia.

We performed 402 primer combinations, and assuming that each competitive PCR reaction gives rise to approximately 100 bands on a DDRT gel and that each band corresponds to one mRNA, this investigation allowed comparison of about 40,000 mRNAs. We excised and sequenced 56 bands, which showed overexpression (ranging from 1-10 fold) in at least one of the CIS samples. Several mRNAs were detected with more than one primer combination; for instance, overexpression of CCND2 was detected with three different primer combinations. The RT-PCR analysis verified overexpression of 24 known genes, 4 transcripts corresponding to ESTs and 1 sequence not annotated as a gene.

Example 3 Antibodies Against the Genes

Several vendors of commercial antibodies were searched for antibodies to the proteins encoded by the identified genes highly expressed in testicular CIS. In addition, new antibodies against protein product of the newly identified CIS markers genes are going to be generated.

Example 4 Identification of Markers for CIS Progression into Seminoma or Non-seminoma

Besides identification of highly specific CIS markers the present inventors also identified markers for the progression of CIS either into seminoma or the non-seminoma. Currently it is not known why some CIS cells give rise to a seminoma and others non-seminomas. It is however speculated that CIS may be predisposed to the one or the other. By identification of the markers for CIS progression together with the CIS markers, the present inventors will be able to: 1) identify CIS cells in a subject 2) predict whether the subject is predisposed to either a seminoma or a non-seminoma, or may develop a combined tumour 3) evaluate to what degree the CIS in the subject has evolved into a seminoma or a non-seminoma 4) monitor during a possible subsequent treatment whether or not all CIS cells or derived tumours have been successfully eradicated.

Example 5 Kit Development

A diagnostic kit for screening for a panel of the marker genes can be provided. Such a kit may be in different forms, depending whether the gene expression in a sample will be screened at the RNA or at the protein level. The most obvious form would be a kit based on reverse transcriptase polymerase chain reaction (RT-PCR). By picking out a battery of the most promising CIS marker genes, RNA purified from a human sample can be tested for the presence of CIS marker genes at the transcript level. The present inventors can also take advantage of the high throughput microarray technique for assaying the expression of hundreds of genes simultaneously. This could be in the format of a microarray focused on genes identified here as CIS markers. Additional microarrays e.g. containing markers for the progression into seminoma or nonseminoma can also be developed.

At the protein level, the present inventors can also develop two approaches: either select a limited number of best markers and make an ELISA-based assay using robust and well validated specific antibodies. The present inventors can also develop a protein-microarray using a large number of antibodies against a broader panel of markers, including those previously known, spotted on a glass slide.

Example 6 New Nuclear Markers

One very important finding from the study of CIS markers at the protein level was to find proteins localized to the nucleus of the CIS cells. This is important because CIS cells shed to seminal fluid are exposed to different pH and high concentrations of proteases that may damage the cell membrane (and the proteins located within, e.g. receptors) before the ejaculation takes place. A nuclear marker will be better retained than a cell surface marker and thus will increase the possibility for detection in semen samples.

Example 7 Human Samples for Detection of CIS

The most convenient and least invasive biological sample to detect CIS cells will be semen (ejaculate). In our earlier studies the present inventors established that some CIS cells are present in semen samples in patients with CIS or overt germ cell tumours in the testes. However, in some cases of early invasion/metastasis, it may also be possible to detect CIS/early tumour cells in a blood sample. Testicular tissue in the form of i.e. biopsies, is nowadays used to detect CIS, and the novel markers can be used to confirm the results of e.g. a CIS array screen, before the final treatment (e.g. orchidectomy) takes place. Yet, other human samples e.g. urine may perhaps be used in the future, e.g. in very young boys, but as only single cells are expected to be detected in urine, careful testing and validation has to be performed.

Example 8 CIS Cells are Embryonic Stem Cell-like

Among the genes highly expressed in CIS, the present inventors noticed a range of genes known to be expressed primarily in embryonic stem cells (ESC) and/or primordial germ cells (PGC), such as POU5F1 DPPA4, DPPA5, and NANOG. The present inventors therefore performed a systematic comparison of genes highly expressed in CIS with genes recently

13; Sperger, J M, et al. Proc Natl Acad Sci USA 2003, 100: 13350-5). As shown in FIG. 4, many of the genes found in ESC were also highly expressed in our CIS samples. Among the 100 highest expressed CIS marker genes (listed in FIG. 1), 34 genes were reported in ESC. The overlap might even be greater, as many of the genes included on the array are yet uncharacterized and thus may be differently annotated on the microarrays used to expression profile ESC. Excluding genes with no functional description (gene name) leads to an approximately 47% overlap. Furthermore, studies where a relative level of expression in ESC cell compared to a reference was reported (Ramalho-Santos, M, et al. Science 2002, 298:597-600;Sperger, J M, et al. Proc Natl Acad Sci USA 2003, 100:13350-5), the ranking of the expression level seemed to correlate between CIS and ESC, though with some exceptions. The studies the present inventors compared with, in addition all have used different reference samples to explore ESC specific genes and therefore not always agree on the expression in ESC (FIG. 4).

Furthermore, the chromosomal distribution of the over-expressed genes in CIS may be associated with a non-random genomic amplification in certain “hot-spot” areas. The present inventors therefore created a map of the chromosomal distribution of the genes highly expressed in CIS. Searching for the chromosomal localization of these genes and normalizing with the length of each chromosome revealed that there was an over-representation of up-regulated genes on chromosomes 7, 12, 14, 15, and especially chromosome 17 (FIG. 5) Plotting the density of up-regulated genes in each chromosomal band allowed us to narrow down hot-spots to smaller regions, with 17q as the most pronounced region. Recurrent genomic gain of chromosomes 17q and 12 was recently discovered in cultured human ESCs (Draper, J S, et al. Nat Biotechnol 2004, 22:53-4; Pera, M F Nat Biotechnol 2004, 22:42-3). It was postulated that cultured ESC might gain extra chromosome material in these areas after freezing and thawing, which could inhibit apoptosis and increase their self-renewal in culture etc. (Draper, J S, et al. Nat Biotechnol 2004, 22:53-4). This again indicates that CIS cells may have strong similarities to embryonic stem cells and the identified CIS markers may thus be used to identify transplanted embryonic stem cells how have evolved into CIS cells leading to uncontrolled growth of the embryonic stem cells.

Example 9 Transcription Factor AP-2γ is a Developmentally Regulated Marker of Testicular Carcinoma In Situ and Germ Cell Tumors Purpose

Transcription Factor Activator Protein-2γ (TFAP2C, AP-2γ) was previously reported in extraembryonic ectoderm and breast carcinomas, but not in the testis. the above gene expression study we detected AP-2γ in carcinoma in situ testis (CIS, or intratubular germ cell neoplasia, IGCN), precursor of testicular germ cell tumors (TGCT). In this example we aimed to investigate the expression pattern of AP-2γ and to shed light on this factor in germ cell differentiation and the pathogenesis of germ cell neoplasia.

Experimental Design

We analyzed expression pattern of AP-2γ at the RNA and protein level in normal human tissues and a panel of tumors and tumor-derived cell lines. In the gonads, we established the ontogeny of expression of AP-2γ in normal and dysgenetic samples. We also investigated the regulation of AP-2γ by steroids and retinoic acid.

Results

We detected abundant AP-2γ in testicular CIS and in TGCTs of young adults, and confirmed differential expression of AP-2γ in somatic tumors. We found that AP-2γ expression was regulated by retinoic acid in an embryonal carcinoma cell-line (NT2). The investigation of ontogeny of AP-2γ protein expression in fetal gonads revealed that it was confined to oogonia/gonocytes and was down-regulated with germ cell differentiation. In some pre-pubertal intersex cases, AP-2γ was detected outside of the normal window of expression, probably marking neoplastic transformation of germ cells.

Conclusions

AP-2γ is developmentally regulated and associated with the undifferentiated phenotype in germ cells. This transcription factor may be involved in self-renewal and survival of immature germ cells and tissue-specific stem cells. AP-2γ is a novel marker of testicular CIS and CIS-derived tumors.

The aim of this study was to explore the possible role of AP-2γ in the pathogenesis of reproductive tumors, especially in the testis, and to further investigate the timing of neoplastic transformation of germ cells. To that end, we determined a comprehensive expression profile of AP-2γ in a large panel of normal tissues, tumors and tumo-derived cell lines, established the ontogeny of AP-2γ in normal and dysgenetic human gonads and studied regulation of the AP-2γ expression in selected cell lines.

MATERIALS AND METHODS Tissue Samples

The Regional Committee for Medical Research Ethics in Denmark approved the use of human tissue samples for the studies of novel genes expressed in germ cell cancer.

The tissue samples from adults with testicular neoplasms were obtained directly after orchidectomy and macroscopic pathological evaluation. Each testicular sample was divided into several tissue fragments, which were either snap-frozen at −80° C. for nucleic acid extraction, or fixed overnight at 4° C. in Stieve's fluid, buffered formalin or paraformaldehyde (PFA), and subsequently embedded in paraffin.

Tissue sections were stained with haematoxylin and eosin (HE) or with antibodies against placental alkaline phosphatase (PLAP or ALPP) for histological evaluation (Giwercman, A, et al. APMIS 1991, 99:586-94).

A series of 31 of overt testicular tumors were analyzed by immunohistochemistry, including classical seminomas, various non-seminomatous tumor components, spermatocytic seminomas, Leydig cell tumors and a testicular B-cell lymphoma (listed in Table III). Moreover 14 samples of testicular CIS were analyzed: twelve, which were from tissue adjacent to a TGCT, and two, which had not progressed to an overt tumor, but only had signs of micro-invasion. Furthermore, we included 8 samples containing normal testicular tissue from either patients with prostate cancer or from tissue surrounding a GCT. A representative panel of tissues adjacent to the microscopically examined samples (seminomas, nonseminomatous tumors and specimens with CIS) was analyzed by RT-PCR and ISH. RNAs for RT-PCR were isolated from homogeneous tumors and from specimens containing the largest possible number of tubules with CIS, as judged by microscopical examination of adjacent tissue fragments.

The series for immunohistochemical analysis of the ontogeny of expression of AP-2γ in normal and dysgenetic gonads included paraffin embedded specimens from tissue archives of the Rigshospitalet, Copenhagen University Hospital. The 40 normal fetal tissue samples (19 testicular and 21 ovarian specimens) were obtained after induced or spontaneous abortions and stillbirths, mainly due to placental or maternal problems. The developmental age was calculated from the date of the last menstrual bleeding, supported by the foot size of the fetus. Normal postnatal testicular samples (N=16) were obtained either from autopsies of infants who died suddenly of causes unrelated to the reproductive system or

individuals with intersex disorders or other components of the testicular dysgenesis syndrome (TDS)(Skakkebaek, N E, et al. Hum Reprod 2001, 16:972-8), and 12 testicular biopsies with mild dysgenetic features (e.g. undifferentiated tubules and/or microliths) with or without CIS, performed for diagnostic reasons from young adult men with sub-fertility or with contralateral germ cell tumors.

In addition 130 samples from extragonadal tissues were examined. Panels of normal tissues and mammary gland tissues with or without neoplastic lesions were investigated using commercial tissue arrays (MaxArray Human Breast Carcinoma and Human Normal Tissue Microarray slides, Zymed, S. San Francisco, Calif., USA). All specimens are listed in Table III.

Studies in Cell Lines

The following established cancer cell lines were grown in standard conditions (5% CO₂ 37° C.): embryonal carcinoma NT2 and 2102EP lines, and a mammary tumor-derived MCF7 line. Total RNA was isolated for RT-PCR as described below, while for the immunohistochemical staining of the protein, the cells were spun in a cyto-centrifuge or directly grown on microscopic slides.

For analysis of the effect of retinoic acid (RA) on the AP-2γ expression (Andrews, P W Dev Biol 1984, 103:285-93), NT2 cells were grown in DMEM medium (10% FBS, 2 mM L-glutamine, 25 IU/ml penicillin, 25 μg/ml streptomycin) and stimulated with 10 μM RA (Sigma-Aldrich, St. Louis, Mo.) for 0-15 days to induce differentiation; 2102Ep cells were grown in DMEM medium with added 100 μM β-mercaptoethanol, and stimulated with 10 μM RA for 0-10 days. A possible estrogen regulation of AP-2γ was analyzed in MCF7 cells, which were grown in steroid-depleted DMEM medium (5% dextran-charcoal stripped FBS, 1× non-essential amino acids, 1 nM insulin, 2 mM L-glutamine, 25 IU/ml penicillin, 25 μg/ml streptomycin) for 6 days and then exposed to 1 nM estradiol, ICI-182,780 (anti-estrogen), or ethanol (vehicle) for 24 or 48 hours.

RT-PCR

Total RNA was purified using the NucleoSpin RNAII kit as described by the manufacturer (Macherey-Nagel, Düren, Germany). RNA samples were DNAse digested, and cDNA was synthesized using a dT₂₀ primer. Specific primers were designed for TFAP2C (TFAP2C-ex6: ATCTTGGAGGACGAAATGAGAT, TFAP2C-ex7: CAGATGGCCTGGCTGCCAA), spanning intron-exon boundaries. RT-PCR was performed in duplex in 30 μl of (final concentrations): 12

expression of the marker gene ACTB was analyzed with the following primers (ACTB-ex4: ACCCACACTGTGCCCATCTA, ACTB-ex6: ATCAAAGTCCTCGGCCACATT). Cycle conditions for all PCR reactions: 1 cycle of 2 min. at 95° C.; 40 cycles of: 30 sec. at 95° C., 1 min. at 62° C., 1 min. at 72° C. and finally 1 cycle of 5 min. at 72° C. PCR products were run on 1.5% agarose gels and visualized by ethidium bromide staining. Fragment size was 205 base pairs for TFAP2C and 815 for ACTB. Representative bands were excised, cloned (with TOPO® Cloning Invitrogen, Carlsbad, Calif., USA) and sequenced for verification.

In Situ Hybridization (ISH)

Probes for ISH were prepared by use of specific primers (1^(st) primer combination: AAGAGTTTGTTACCTACCTTACT, CATCAATTGACATTTCAATGGC, 2^(nd) primer combination AATTAACCCTCACTAAAGGGTTAAAGAGCCTTCACT,

TAATACGACTCACTATAGGGCTAAGTGTGTGG) containing an added T3- or T7-promotor sequence, respectively (promotor sequences underlined). PCR conditions were: 5 min. 95° C.; 5 cycles of: 30 sec. 95° C., 1 min. 45° C., 1 min. 72° C.; 20 cycles of 30 sec. 95° C., 1 min. 65° C., 1 min. 72° C. and finally 5 min. 72° C. The resulting PCR product was purified on a 2% low melting point agarose gel and sequenced from both ends, using Cy5-labelled primers complementary to the added T3 and T7 tags. Aliquots of about 200 ng were used for in vitro transcription labeling, using the MEGAscript-T3 (sense) or MEGAscript-T7 (anti-sense) kits, as described by the manufacturer (Ambion, Houston, Tex., USA). The composition of the 10×-nucleotide mix was: 7.5 mM ATP, GTP and CTP, 3.75 mM UTP, 1.5 mM biotin-labeled UTP. To estimate quantity and labeling efficiencies, aliquots of the labeled RNA product were analyzed by agarose gel electrophoresis, dotted onto nitrocellulose filters and developed. ISH was performed on 3-6 different samples as described previously (Hoei-Hansen, C E, et al. Mol Hum Reprod 2004, 10:423-31).

Immunohistochemistry

A commercially available monoclonal anti-AP-2γ antibody (6E4/4:sc-12762, kindly provided for testing by Santa Cruz Biotechnology Inc., Santa Cruz, Calif., USA) was used. The antibody was validated by western blots by the manufacturer. In addition, several other antibodies were used as controls, in particular to detect CIS cells (anti-PLAP, a monoclonal antibody from BioGenex, San Ramon, Calif., USA; anti-OCT3/4, C-20, sc 8629, Santa Cruz Biotechnology), and to control for integrity of fetal and infantile testis samples obtained at autopsies (anti-AMH, a monoclonal antibody kindly provided by R. Cate, Biogen). The immunohistochemical staining was performed using a standard indirect peroxidase method, as previously described for other antibodies (Giwercman, A, et al. APMIS 1991,

fixed in formalin or PFA were heated in a 5% urea, pH 8.5, whereas sections fixed in Stieve's fluid were heated in TEG buffer, pH 9.0 (TRIS 6.06 g/5L, EGTA 0.95 g/5L). Subsequently, the sections were incubated with 0.5% H₂O₂ to inhibit the endogenous peroxidase, followed by diluted non-immune goat serum (Zymed, S. San Francisco, Calif., USA) to block unspecific binding sites. The incubation with the primary anti-AP-2γ antibody diluted 1:25-1:100 was carried out overnight at 4° C. For tissues fixed in Stieve's fluid the primary antibody was diluted in Background Reducing antibody diluent (DakoCytomation, Glostrup, Denmark). For negative control, a serial section from each block was incubated with a dilution buffer. Subsequently, a secondary biotinylated goat-anti-mouse link antibody was applied (Zymed, S. San Francisco, Calif., USA), followed by the horseradish peroxidase-streptavidin complex (Zymed, S. San Francisco, Calif., USA). Between all steps the sections were thoroughly washed. The bound antibody was visualized using aminoethyl carbazole substrate (Zymed, S. San Francisco, Calif., USA). Most sections were lightly counterstained with Mayer's haematoxylin to mark unstained nuclei.

The sections were examined under a light microscope (Zeiss) and scored systematically by two investigators (CHH and ERM). The staining was assessed using an arbitrary semi-quantitative score of the percentage of cells stained in a section and their staining intensity: +++: strong staining, ++: moderate staining, +: weak staining, +/−: very weak staining, neg: no positive cells detected.

RESULTS AP-2γ is a New Marker for Testicular Carcinoma In Situ and Derived Germ Cell Tumors

After the discovery of the high expression of AP-2γ in testicular tissues harboring CIS cells (5), we extensively mapped the expression at the mRNA level by reverse transcriptase PCR (RT-PCR) in a panel of testicular neoplasms and tumor-derived cell lines. Subsequently, we determined cellular localization of AP-2γ transcripts by in situ hybridization (ISH), and at the protein level by immunohistochemistry in a comprehensive panel of normal and neoplastic tissues.

RT-PCR showed a high expression of AP-2γ in samples of seminoma, teratoma, embryonal carcinoma and CIS as compared to normal testicular tissue, which showed only a trace of reaction in one biopsy from a patient with an adjacent TGCT, and could encompass a few CIS or micro-invasive tumor cells (FIG. 8). Expression in CIS cells was approximately equivalent in tissue containing CIS adjacent to overt tumors and in CIS at the micro-invasive stage. For a few CIS and tumor samples the expression was confirmed in the

al. Mol Hum Reprod 2004, 10:423-31)(results not shown). ISH revealed cytoplasmic staining in CIS cells, seminoma, embryonal carcinoma and to lesser extent in some components of teratomas (FIG. 9). ISH in normal testicular tissue was not completely conclusive; in contrast to IHC, which did not show any detectable protein in normal germ cells, a reaction was observed in some spermatocytes and spermatids (results not shown). The presence of TFAP2C transcripts in the normal germ cells with a simultaneous lack of the protein product cannot, therefore, be excluded. This could be due to translational regulation of AP-2γ in the testis. A similar discrepancy between expression at the mRNA and the protein level was previously described for AP-2α in colon cancer (Ropponen, K M, et al. J Clin Pathol 2001, 54:533-8). Immunohistochemistry demonstrated a high abundance of AP-2γ protein in CIS. CIS cells adjacent to TGCTs were uniformly strongly positive for AP-2γ regardless of the tumor type, and equally strong in CIS present in the testis and as an isolated pre-malignant lesion. Gonadoblastoma, a CIS-like pre-malignant lesion of severely dysgenetic gonads was also strongly positive (FIG. 10). Differential expression was however observed in the overt TGCTs: seminomas were strongly positive, whereas a heterogeneous pattern was detected in the non-seminomas (FIG. 9). Embryonal carcinoma demonstrated strongest staining, teratomas displayed staining in some epithelial and stromal elements but many highly differentiated components were negative. In all TGCT specimens staining was present exclusively in the nucleus. No expression was detected in spermatocytic seminoma. In non-germ-cell-derived testicular tumors no expression was detected in a B-cell lymphoma and two Leydig cell tumors (one testicular and one adrenal). One Leydig-Sertoli cell tumor was unexpectedly positive, however, as the staining was confined to the cytoplasm, this may be an unspecific reaction, which is quite frequently observed for various antibodies in the protein and glycoprotein-filled Leydig cells. A similar but much weaker unspecific staining in Leydig cell cytoplasm was also observed in a few specimens of testicular parenchyma. In general, the intensity of staining varied somewhat depending on the fixative used, with stronger staining in tissues fixed with PFA and formalin compared to those fixed in Stieve's and Bouin. In addition, in samples fixed in Stieve's fluid or in high-percentage formalin, there was a tendency to an unspecific staining of erythrocytes. The complete results of the immunohistochemical staining are listed in Table III and representative examples are shown in FIGS. 9, 10 and 11.

The expression of AP-2γ is Developmentally Regulated in Human Gonads

To investigate whether the high expression of AP-2γ in CIS cells is linked to their gonocyte-like phenotype, as is the case for a number of other markers for CIS cells (Rajpert-De

of expression of AP-2γ by immunohistochemistry in a panel of specimens of normal human fetal testis and ovaries during development.

The AP-2γ protein was detected in almost all gonocytes in testes from 10 weeks of gestation (earlier samples were not available) until approximately 22 weeks of gestation (FIG. 10), although a few of our analyzed tissue samples failed to show expression. Expression was gradually reduced after week 22, but persisted in a few cells until approximately 4 months of postnatal age. Afterwards, AP-2γ protein was not detected in spermatogonia in normal pre-pubertal, post-pubertal or adult testes.

In fetal ovaries AP-2γ expression was seen in oogonia in high amounts in early gestational ages and to a lesser extent in third trimester. The number of positive oogonia was decreasing with the increasing number of oocytes that entered the meiotic prophase, which were AP-2γ negative. No expression was seen in adult ovary, but only few samples were analyzed.

Changes of the Expression Pattern of AP-2γ in Intersex and Dysgenetic Gonads

Subsequently, we asked the question whether or not the normal developmental pattern of the expression of AP-2γ is changed in testicular dysgenesis and disorders of sex differentiation, conditions with a markedly increased risk of germ cell neoplasia. Expression of AP-2γ in dysgenetic gonads was analyzed only by immunohistochemistry, because the specimens were available only as paraffin-embedded blocks from tissue archives. The pattern of expression in these specimens was in general similar to that in the normal testes, but in some samples expression deviated from the observed pattern. Expression of AP-2γ was not observed in a sample from a male fetus gestational age 15 weeks with mosaic isochromosome Y, similar to previously observed lack of OCT3/4 (Rajpert-De Meyts, E, et al. Hum Reprod 2004). Staining for AMH was positive, suggesting that the integrity of proteins should be preserved in the sample. Prolonged expression of AP-2γ was seen in cells resembling gonocytes in testicular cords in an ovotestis from a 14-month old XX hermaphrodite, but not in the oocytes present in the ovarian part. In a few of the dysgenetic samples neoplastic, pre-invasive CIS or gonadoblastoma was present and these showed a high expression of AP-2γ. In three cases staining was observed in foci of germ cells that morphologically were classified as somewhere in between gonocytes and CIS (see FIG. 10). In two of the cases (girls with AIS of age 9 months and 6 years, respectively) PLAP was also positive. The third was from a testis removed from a 2-year old girl with AIS, where a very small focus of AP-2γ positive cells was detected. We were not able to locate this focus morphologically in adjacent sections cut before and after, and stainings with PLAP and OCT3/4 were accordingly negative.

Expression of AP-2γ is Associated with Cell Differentiation or Proliferation and is Cell Type Dependent

In order to define the extent of expression and a possible link to hormonal stimulation, expression of AP-2γ was analyzed in some tissues that are endocrinologically activated and in a panel of normal somatic tissues. In normal female mammary tissue expression was seen in a subpopulation of basally situated epithelial duct cells, and expression was also detected in some, but not all, premalignant or manifest malignant changes in the female breast (FIG. 11, Table III). In samples from skin, the basal layer of keratinocytes was positive, and weaker staining could be seen in the adjacent layers of epidermis (FIG. 11), which is in concert with the previously reported pattern. In normal adult kidney AP-2γ expression was seen in a subset of cells in proximal tubules. Finally, AP-2γ expression was present in lung tissue, in pneumocytes lining alveoles. All other analyzed tissue samples were negative (Table III). We cannot exclude that the AP-2γ expression may be developmentally regulated in some tissues, in analogy to the testis. We could not gain access to a full spectrum of human fetal tissues at different developmental stages, but we have examined and found no AP-2γ expression in the following fetal tissues from the first or second trimester of gestation: epididymis, liver, heart, thymus, thyroid gland, kidney and adrenal gland.

Finally, regulation of AP-2γ expression was studied in vitro in three cell lines. We showed by RT-PCR that AP-2γ was RA-regulated in NT2 cells in a biphasic manner. Strong expression was observed in cells without RA-induced differentiation, after 3 days of RA treatment (which at that point induced cell proliferation) the expression was somewhat stronger and then declined after 15 days when the cells have differentiated (FIG. 8). A heterogeneous staining for AP-2γ protein was seen in NT2 cells by immunocytochemistry in all analyzed samples, regardless of the length of RA treatment. It was not possible to establish the pattern quantitatively, because of differences in Intensity from cell to cell. In contrast, in the 2102Ep cells, which do not differentiate with RA treatment, expression was unaffected by RA treatment at the RNA level, and immunocyto-chemical staining was uniformly strong in all analyzed cells. In MCF7 cells, expression was similar in cells exposed to estraciol, the arti-estrogen ICI, or ethanol, both at the RNA level, and at the protein level, where expression was seen in a subset of cells in all analyzed cells, regardless of treatment (

). For examples of RT-PCR results, see FIG. 8.

DISCUSSION

In the present study we comprehensively investigated the pattern of expression of the transcription factor AP-2γ, and established AP-2γ as a novel marker for neoplastic germ cells, including testicular carcinoma in situ, the common precursor of TGCTs. Furthermore, we discovered that AP-2γ was developmentally regulated in human gonads, with marked differences between the testes and ovaries.

Our investigations of the pattern of expression of AP-2γ in extra-gonadal normal and neoplastic tissues were largely in concert with previous studies, thus confirming the specificity of the antibody. The transcription factor was preferentially expressed in proliferating immature cells, which retained tissue-specific stem cell characteristics, suggesting a putative oncogenic function of AP-2γ.

In the testis, we found that the AP-2γ protein was expressed in early gonocytes but not in any cell type in the pre- or post-pubertal testis. The expression rapidly declined from approximately 22 weeks of gestation, and was gradually lost while gonocytes differentiated into infantile spermatogonia up to about 4 months of postnatal age, when the final stage of this differentiation takes place, probably stimulated by the hormonal surge at the “mini-puberty” (Andersson, A M, et al. J Clin Endocrinol Metab 1998, 83:675-81;Hadziselimovic, F, et al. J Urol 1986, 136:274-6). Interestingly, in a few pre-pubertal intersex cases, AP-2γ was observed in a subset of gonocytes outside the normal window of expression. This prolonged expression may reflect a delay in differentiation but may perhaps be a marker of the initiation of neoplastic transformation of these immature germ cells into “pre-CIS” cells, which then may further transform to a typical CIS pattern at the onset of puberty. In the ovary, AP-2γ protein was confined to oogonia and was riot detectable after meiotic entry in oocytes. This pattern of expression suggests that the protein plays a role exclusively in undifferentiated germ cells. Analyses in cell lines confirmed that AP-2γ was most abundant in undifferentiated cells, as expression of the transcript was down-regulated after a transient induction in AP-2γpositive NT-2 cells treated with RA for up to 15 days. In cells that do not differentiate (2102Ep) expression was constantly high. Oulad-Abdelghani and colleagues (Oulad-Abdelghani, M, et al. Exp Cell Res 1996, 225:338-47) reported a transient rise in AP-2γ levels with a peak after 12 hours of RA treatment in embryonal carcinoma derived P19 cells, but did not analyze levels beyond 24 hours. An association of AP-2γ with an immature state of germ cells was also observed in overt TGCTs, where classical seminoma and embryonal carcinoma were strongly positive, while highly differentiated somatic elements of teratomas were negative. Spermatocytic seminoma, which is not derived from CIS but from mature spermatogonia, was also AP-2γ-negative. negative. Overall, the pattern of expression of AP-2γ in TGCTs resembles that of KIT and CCT-4, which are also associated with an undifferentiated state and pluripotency, typical for cells retaining some stem cell like features. The high expression of AP-2γ in CIS

cell. In adult testes AP-2γ was only seen either in CIS or in overt TGCTs, or in rare specimens harboring dysgenetic features, and in the latter only in gonadoblastoma and CIS cells. Thus, AP-2γ can be added to a list of markers for germ cell neoplasms that are also present in gonocytes but not detectable in the normal adult testis, such as PLAP, KIT or OCT-4 (Rajpert-De Meyts, E, et al. APMIS 2003, 111:267-78; discussion 278-9).

Besides an inverse association with cell differentiation, which was also noted by others in other cell systems (Jager, R, et al. Mol Cancer Res 2003, 1:921-9), very little is known concerning the biological function and the mechanism of action of AP-2γ, especially in germ cells. The most interesting question is what are the gene targets for AP-2γ in germ cells, and with which other proteins does this transcription factor interact. In other cell types AP-2γ has been previously shown to interact with a number of genes that are also highly expressed in CIS cells, e.g. IGF-binding protein 5 (Jager, R, et al. Mol Cancer Res 2003, 1:921-9) or KIT (Rajpert-De Meyts, E, et al. Int J Androl 1994, 17:85-92). KIT appears to be of particular interest, as it was reported to be down-regulated in several types of tumors derived from tissues that express AP-2γ, e.g. breast cancer, colorectal cancer or melanoma (Ropponen, K M, et al. J Clin Pathol 2001, 54:533-8).

Estrogen signaling is another possible candidate pathway which could be regulated by AP-2γ, as is suggested by its expression in the epithelium of milk ducts and the association with some forms of breast cancer. While the classic estrogen receptor (ERα) is not expressed in the testis (neither in the fetal life or adulthood), the ERβ is expressed in human fetal testis in the second trimester, and gonocytes are potential targets for estrogen action. This is of interest because it has been suggested that inappropriate exposure to estrogens during fetal life may have an impact on the development of CIS and TGCTs (Skakkebaek, N E, et al. Hum Reprod 2001, 16:972-8). Furthermore, the progression from CIS into an overt TGCT occurs after the endocrinological surge of puberty, when the intra-testicular levels of steroid hormones rise markedly. In the current study, we have analyzed the expression of AP-2γ in a breast tumor-derived cell line, MCF7, which is estrogen dependent. We have not observed any changes in expression, neither after treatment with estradiol, nor an anti-estrogen. This is in disagreement with a recent study (Orso, F, et al. Biochem J 2004, 377:429-38), which showed induction of AP-2γ by estrogens in several breast tumor cell lines. Whether AP-2γ is indeed involved in estrogen signaling remains an unresolved issue, since existing reports are partially contradictory and will require further investigations. We need also to keep in mind that the function of AP-2γ may be cell-type specific, as was demonstrated recently for the transcriptional activation of the ERBB2 gene (Vernimmen, D, et al. 3rd Cancer 2003, 89:899-906) and

In summary, our investigations suggest a role for AP-2γ in pathways regulating cell differentiation, including in fetal gonocytes, which was not previously known. Frequent expression of AP-2γ in various malignancies suggests that the pathways may be involved in oncogenesis. Finally, developmental expression of this transcription factor in the testis makes AP-2γ a very promising new marker for diagnosis of early stages of germ cell neoplasia.

Example 10 Early Diagnosis of Pre-invasive Testicular Germ Cell Neoplasia by Immunocytological Detection of AP-2γ-positive Cells in Semen Samples

In the above genome-wide gene expression profiling study of CIS cells, we have identified a number of genes expressed also in embryonic stem cells and foetal gonocytes but not in adult germ cells, thus providing many possible new markers for CIS.

One of such genes was TFAP2C (mapped to chromosome 20q13.2), which encodes the transcription factor activator protein-2 (AP-2γ). We established AP-2γ as a novel marker for foetal gonocytes and neoplastic germ cells, including testicular CIS, with a role in pathways regulating cell differentiation and a possible involvement in oncogenesis. The fact that AP-2γ protein was not expressed in normal adult reproductive tract but was abundant in nuclei of CIS and tumour cells, which are better protected than the cytoplasm from degradation in semen due to a structural strength, prompted us to analyse the value of AP-2γ for detection of CIS and/or tumour cells in ejaculates in a series of patients and controls. The local ethics committee approved the study and participants gave written informed consent.

The present example presents a new non-invasive method capable of detecting testicular cancer at the pre-invasive carcinoma in situ (CIS) in a semen sample. The assay is based on immunocytological staining of semen samples for transcription factor AP-2γ, previously identified as a marker for neoplastic germ cells.

In an investigation of 104 andrological patients, cells positive for AP-2γ were found only in semen samples from patients diagnosed a priori with testicular neoplasms and in a 23-year-old control subject with oligozoospermia and no symptoms of a germ cell tumour (FIG. 7). Testicular biopsies performed during the follow-up of this patient revealed widespread CIS in one testis, thus proving a diagnostic value of the new assay. Optimisation of the method is in progress, but a preliminary assessment gives promise that the method may have a place in screening of germ cell neoplasia in at-risk patients.

The number of patients that we have screened for the presence of immunoreactive AP-2γ is

have tested 347 andrological patients (including the 104 mentioned above) and found CIS-like cells positive for AP-2γ in semen samples of 3 patients, including the first case described above (a 23-year-old subfertile control subject with widespread CIS confirmed by testicular biopsies). Two other patients are currently under clinical follow-up and being considered for testicular biopses.

Materials and Methods

A semen sample from each patient was diluted if necessary, divided in portions of 100 μl, spun down on a microscope slide with 400 μl PBS buffer, dried, fixed 10 min in formalin, washed and dried again. The immunocytochemical staining was performed with the monoclonal anti-AP-2γ antibody (6E4/4:sc-12762, Santa Cruz Biotechnology Inc., Santa Cruz, Calif., USA) using a standard indirect peroxidase method, as previously described (Almstrup, K, et al. Cancer Res 2004, 64:4736-43), except for small modifications tested using control semen samples spiked with AP-2γ-positive seminoma cells (FIG. 7A). For negative control, another cytospin was incubated with a dilution buffer, and for positive control AP-2γ-positive seminoma cells were used. Staining was scored using an arbitrary 0-5 scale based on the intensity and morphological resemblance of stained elements to CIS or tumour cells: Score 0—no staining, 1—negative with some unspecific particles stained, 2—trace reaction in small fragments of nucleus-resembling structures, 3—clear staining in a part of a nucleus, with correct morphology, 4—clear staining in a whole nucleus, with correct morphology, 5—two or more cells with score 4. Scores 0-2 were classified as negative, while 3-5 were classified as positive.

Results

At the evaluation of one of the first series of semen samples, we detected six AP-2γ-positive cells in a sample from one of the control participants (FIG. 7B). He was a 23-year-old man that presented for routine semen analysis due to the infertility problem in the couple. The presence of one small testis and a very poor semen quality in combination with the finding of AP-2γ stained cells constituted a well-justified indication for bilateral open testicular biopsies, which were performed in agreement with the patient. The right-sided biopsy demonstrated normal testicular tissue, whereas the left-sided biopsy revealed numerous tubules containing CIS, which was confirmed with PLAP and AP-2γ staining (FIG. 7D, E). The patient was advised to undergo unilateral orchidectomy, prior to which semen was cryopreserved.

A preliminary assessment of the value of the AP-2γ immunoassay was subsequently done after analysis of semen samples from 104 patients: 12 patients with CIS or testicular

testicular cancer patients after operation (none had contralateral CIS), 12 patients with other diseases (e.g. referred for semen cryopreservation before treatment for non-testicular cancers and diseases) and 73 healthy or subfertile control patients.

The results are summarised in Table II and examples are shown in FIG. 7. We detected AP-2γ-positive cells in 5 of 12 patients harbouring a priori diagnosed testicular neoplasia, giving a sensitivity of our assay of 42%. However, after addition of the newly diagnosed control patient with CIS, the sensitivity is 46% (95% CI, 23 to 71%). It is especially noteworthy that we did not detect false positive staining among the healthy controls and patients with other cancers, suggesting a high specificity of the assay.

The large proportion of negative results in the testicular cancer patients could be due to a small volume of the semen sample used for the test (50-300 μl out of total normal volume 3-5 ml, depending on concentration and number of samples), thus stressing the need for either repeated analysis or larger volume analysed. Negative results could also be due to compression from the tumour causing obstruction of seminiferous tubules resulting in few or no CIS cells shed into semen. However, considering the variability of the number of CIS cells present in the tissue adjacent to a tumour, the sensitivity of our assay is reasonably good, as nearly half of the patients harbouring testicular germ cell neoplasm have been detected in this preliminary study.

The relatively low sensitivity nevertheless leaves room for improvement and further optimisation of the method is currently in progress. The results of planned studies in a wider panel of patients will confirm whether this assay should be offered widely to patients at risk for TGCT as a method of non-invasive screening for CIS. Such screening could be performed, for example, at andrology and fertility clinics in young men with atrophic testes, history of cryptorchidism or in need for an assisted reproduction technique. If diagnosis of testicular cancer is made at the pre-invasive CIS stage, the patient can be offered the most gentle and optimal treatment.

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1. A method for determining the presence of precursors of germ cell tumours in a sample, said method comprising: a) determining the expression profile of a group of markers in said sample, wherein the group of markers consists of at least one marker selected independently from the markers listed in table 1; b) comparing said expression profile with a reference expression profile; c) identifying whether the expression profile is different from said reference expression profile; and evaluating whether the sample contains precursors of germ cell tumours if the expression profile is different from the reference expression profile.
 2. A method for determining the presence of precursors of germ cell tumours in a sample, said method comprising: a) determining the intensity signal of the proteins encoded by each of the members of the group of markers in said sample, wherein the group of markers consists of at least one marker selected independently from the markers listed in table 1; b) comparing each individual intensity signal with a corresponding reference intensity signal; c) identifying whether each individual intensity signal is different from said corresponding reference intensity signal and evaluating whether the sample contains precursors of germ cell tumours if the intensity signal is different from the corresponding reference intensity signal.
 3. The method according to claim 1, wherein the group of markers is any one of SEQ ID NO 1-156, or SEQ ID NO
 157. 4. The method according to claim 1, wherein the group of markers consists of at least one marker, which in a sample with CIS in 100% of the seminiferous tubules, is up-regulated more than 7 fold when compared to a reference sample.
 5. The method according to claim 1, wherein the expression profile distinguishes between classical seminoma and non-seminoma, in gonads or in extra-gonadal localizations.
 6. A method for monitoring progression from precursors of germ cell tumours to overt cancer cells in an individual, comprising: a) determining the expression profile of a group of markers in said sample, wherein the group of markers consists of at least one marker selected independently from the markers listed in table 1; b) comparing said expression profile with a reference expression profile; c) identifying whether the expression profile is different from said reference expression profile; and evaluating the development stage of precursors of germ cell tumours to overt cancer cells if the expression profile is different from the reference expression profile.
 7. A method for monitoring progression from precursors of germ cell tumours to overt cancer including in an individual, comprising: a) determining the intensity signal of the proteins encoded by each of the members of the group of markers in said sample, wherein the group of markers consists of at least one marker selected independently from the markers listed in table 1; b) comparing each individual intensity signal with a corresponding reference intensity signal; c) identifying whether each individual intensity signal is different from said corresponding reference intensity signal; and evaluating the development stage of precursors of germ cell tumours to overt cancer cells if the intensity signal is different from the corresponding reference intensity signal.
 8. The method according to claim 6, wherein said method distinguishes seminoma from non-seminoma.
 9. The method according to claim 6, wherein said method distinguishes seminoma from CIS.
 10. The method according to claim 6, wherein said method distinguishes non-seminoma from CIS.
 11. A method of identifying precursors of germ cell tumours in a sample from a mammal, the method comprising: assaying said sample by a quantitative detection assay and determining the expression profile or the intensity signal(s) of at least one marker selected from SEQ ID NO:1 SEQ ID NO 254, or SEQ ID NO 255, comparing said expression profile or the intensity signal(s) with reference value(s); identifying whether the expression profile or the intensity signal(s) of at least one marker from the sample is significantly different from the reference value; and evaluating whether the sample contains precursors of germ cell tumours if the expression profile or the intensity signal(s) is different from the reference value.
 12. A method for determining the presence of precursors of germ cell tumours in an individual comprising detecting the presence or absence of at least one expression product, wherein said at least one expression product comprises a nucleotide sequence selected from SEQ ID NO 1-254 or SEQ ID NO 255 in a sample isolated from the individual.
 13. A method of assessing the efficacy of a therapy for inhibiting precursors of germ cell tumours in a subject, the method comprising: comparing the expression profile of a group of markers in a first sample obtained from the subject prior to providing at least a portion of the therapy to the subject and the expression profile of a group of markers in a second sample obtained from the subject following provision of the portion of the therapy, wherein a significantly altered expression profile of the marker(s) in the second sample, relative to the first sample, is an indication that the therapy is efficacious for inhibiting precursors of germ cell tumours in the subject, wherein the group of markers consists of markers selected independently from the markers listed in table 1 and whereby the number of markers in the group is between 1 and
 255. 14. A method of assessing the efficacy of a therapy for inhibiting precursors of germ cell tumours in a subject, the method comprising: comparing the intensity signal of the proteins encoded by a group of markers in a first sample obtained from the subject prior to providing at least a portion of the therapy to the subject and the intensity signal of the proteins encoded by a group of markers in a second sample obtained from the subject following provision of the portion of the therapy, wherein a significantly altered intensity signal of the proteins encoded by the marker(s) in the second sample, relative to the first sample, is an indication that the therapy is efficacious for inhibiting precursors of germ cell tumours in the subject, wherein the group of markers consists of markers selected independently from the markers listed in table 1 and whereby the number of markers in the group is between 1 and
 255. 15. A method for analysing the presence of undifferentiated stem cells highly likely to progress to precursors of germ cell tumours or cancer in an individual, said method comprising a) determining the expression profile of a group of markers in said sample, wherein the group of markers consists of at least one marker selected independently from the markers listed in table 1; b) comparing said expression profile with a reference expression profile; c) identifying whether the expression profile is different from said reference expression profiles; and evaluating whether the sample contains undifferentiated stem cells highly likely to progress to precursors of germ cell tumours or cancer in the individual if the expression profile is different from the reference expression profile.
 16. A method for analysing the presence of undifferentiated stem cells highly likely to progress to precursors of germ cell tumours or cancer in an individual, said method comprising: a) determining the intensity signal of the proteins encoded by each of the members of the group of markers in said sample, wherein the group of markers consists of at least one marker selected independently from the markers listed in table 1; b) comparing each individual intensity signal with a corresponding reference intensity signal; c) identifying whether each individual intensity signal is different from said corresponding reference intensity signal; and evaluating whether the sample contains undifferentiated stem cells highly likely to progress to precursors of germ cell tumours or cancer in the individual if the intensity signal is different from the reference expression profile.
 17. The method according to claim 1, wherein the marker is selected from the group consisting of AP-2γ, PIM-2, TCL1A, NANOG, and E-cadherin. 18-22. (canceled)
 23. The method according to claim 16, wherein the intensity signal is determined by immunocytological detection.
 24. (canceled)
 25. A kit comprising a means to detect a marker listed in table
 1. 